GSM3477045	Larvae_L3	NA	GSE122639		whole worms		 L3	 15eh1	H3K27ac	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	H3K27ac X;V L3 rep1 ChIP-seq	bd_0_1_2_6_ce10	UsingSRR
GSM3477046	Larvae_L3	NA	GSE122639		whole worms		 L3	 15eh1	H3K27ac	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	H3K27ac X;V L3 rep2 ChIP-seq	bd_0_1_2_6_ce10	UsingSRR
GSM3477042	Larvae_L3	NA	GSE122639		whole worms		 L3	 15eh1	DPY-27	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	DPY-27 X;V L3 rep2 ChIP-seq	bd_0_1_2_6_ce10	UsingSRR
GSM3477041	Larvae_L3	NA	GSE122639		whole worms		 L3	 15eh1	DPY-27	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	DPY-27 X;V L3 rep1 ChIP-seq	bd_0_1_2_6_ce10	UsingSRR
GSM2756647	Larvae_L3	NA	GSE103177		whole worms			 stage L3		ATAC-Seq	ce6	ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version dm6 of the fly genome or ce16 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5¡¯ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. All reads that intersected ENCODE blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists ) were removed. Signal bigwig files for ATAC-Seq were generated using JAMM signal generator pipeline (Ibrahim et al., 2015).	whole L3 worm ATAC-seq rep2	bw_0_1_2_4_ce6	GSM2756647_l3worm_ATAC_copy.bw
GSM2756646	Larvae_L3	NA	GSE103177		whole worms			 stage L3		ATAC-Seq	ce6	ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version dm6 of the fly genome or ce16 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5¡¯ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. All reads that intersected ENCODE blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists ) were removed. Signal bigwig files for ATAC-Seq were generated using JAMM signal generator pipeline (Ibrahim et al., 2015).	whole L3 worm ATAC-seq rep1	bw_0_1_2_4_ce6	GSM2756646_l3worm_ATAC.bw
GSM3141761	Larvae_L3	NA	GSE114494		L3 larvae			 N2	H3K4me1	ChIP-Seq	ce10	ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa.	H3K4me1_wt_l3_rep2	bd_0_1_2_6_ce10	UsingSRR
GSM3141760	Larvae_L3	NA	GSE114494		L3 larvae			 N2	H3K4me1	ChIP-Seq	ce10	ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa.	H3K4me1_wt_l3_rep1	bd_0_1_2_6_ce10	UsingSRR
GSM3141727	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		ATAC-Seq	ce10	Reads were trimmed using trim_galore, and aligned using bwa in single-end mode.	wt_L3_ATAC-seq_rep2	bd_0_1_2_6_ce10	UsingSRR
GSM3141726	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		ATAC-Seq	ce10	Reads were trimmed using trim_galore, and aligned using bwa in single-end mode.	wt_L3_ATAC-seq_rep1	bd_0_1_2_6_ce10	UsingSRR
GSM3142709	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_800U_ml	bw_0_1_2_4_ce10	GSM3142709_dnase_wt_l3_rep2_800U_ml.bw
GSM3142708	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_400U_ml	bw_0_1_2_4_ce10	GSM3142708_dnase_wt_l3_rep2_400U_ml.bw
GSM3142707	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_200U_ml	bw_0_1_2_4_ce10	GSM3142707_dnase_wt_l3_rep2_200U_ml.bw
GSM3142706	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_100U_ml	bw_0_1_2_4_ce10	GSM3142706_dnase_wt_l3_rep2_100U_ml.bw
GSM3142705	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_50U_ml	bw_0_1_2_4_ce10	GSM3142705_dnase_wt_l3_rep2_50U_ml.bw
GSM3142703	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_10U_ml	bw_0_1_2_4_ce10	GSM3142703_dnase_wt_l3_rep2_10U_ml.bw
GSM3142704	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_25U_ml	bw_0_1_2_4_ce10	GSM3142704_dnase_wt_l3_rep2_25U_ml.bw
GSM3142702	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_5U_ml	bw_0_1_2_4_ce10	GSM3142702_dnase_wt_l3_rep2_5U_ml.bw
GSM3142701	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep2_2.5U_ml	bw_0_1_2_4_ce10	GSM3142701_dnase_wt_l3_rep2_2.5U_ml.bw
GSM3142700	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep1_800U_ml	bw_0_1_2_4_ce10	GSM3142700_dnase_wt_l3_rep1_800U_ml.bw
GSM3142699	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep1_400U_ml	bw_0_1_2_4_ce10	GSM3142699_dnase_wt_l3_rep1_400U_ml.bw
GSM3142698	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep1_200U_ml	bw_0_1_2_4_ce10	GSM3142698_dnase_wt_l3_rep1_200U_ml.bw
GSM3142697	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep1_100U_ml	bw_0_1_2_4_ce10	GSM3142697_dnase_wt_l3_rep1_100U_ml.bw
GSM3142693	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep1_2.5U_ml	bw_0_1_2_4_ce10	GSM3142693_dnase_wt_l3_rep1_2.5U_ml.bw
GSM3142696	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep1_50U_ml	bw_0_1_2_4_ce10	GSM3142696_dnase_wt_l3_rep1_50U_ml.bw
GSM3142695	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep1_25U_ml	bw_0_1_2_4_ce10	GSM3142695_dnase_wt_l3_rep1_25U_ml.bw
GSM3142694	Larvae_L3	NA	GSE114494		L3 larvae			 wild-type N2		DNase	ce10	Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode.	wt_L3_DNase-seq_rep1_10U_ml	bw_0_1_2_4_ce10	GSM3142694_dnase_wt_l3_rep1_10U_ml.bw
GSM2545810	Larvae_L3	NA	GSE96908	 whole animal	whole animal L3 stage		 L3	 sgIs1 (Strain F)	L3 ChiP-seq	ChIP-Seq	ce6	ChIP sequence fragments were mapped to the C. elegans genome (version ce6) using the Short Read Mapping Package (SHRiMP) alignment tool using the R/Bioconductor package BSgenome.Celegans.UCSC.ce6	L3 ChiP-seq	bd_0_1_2_6_ce10	UsingSRR
GSM1843698	Larvae_L3	NA	GSE71720		L3 staged worms_ELT2_ChIP-seq		 L3 staged worms	 N2	a-ELT-2 	ChIP-Seq	ce10	Quality filtering: Sequenced reads were trimmed of barcodes (FASTX-Toolkit, 11sep2008, http://hannonlab.cshl.edu/fastx_toolkit/index.html) and filtered for primer and adapter sequences using Tagdust (1.12), (Lassmann et al., 2009).	EO037_rep2_ELT2	bw_0_1_2_4_ce10	GSM1843698_08_EO037_rep2_ELT2.bw
GSM1843694	Larvae_L3	NA	GSE71720		L3 staged worms_ELT2_ChIP-seq		 L3 staged worms	 N2	a-ELT-2 	ChIP-Seq	ce10	Quality filtering: Sequenced reads were trimmed of barcodes (FASTX-Toolkit, 11sep2008, http://hannonlab.cshl.edu/fastx_toolkit/index.html) and filtered for primer and adapter sequences using Tagdust (1.12), (Lassmann et al., 2009).	EO025_rep1_ELT2	bw_0_1_2_4_ce10	GSM1843694_08_EO025_rep1_ELT2.bw
GSM1843701	Larvae_L3	NA	GSE71720		L3 staged worms_ELT2_ChIP-seq		 L3 staged worms	 N2	a-ELT-2 	ChIP-Seq	ce10	Quality filtering: Sequenced reads were trimmed of barcodes (FASTX-Toolkit, 11sep2008, http://hannonlab.cshl.edu/fastx_toolkit/index.html) and filtered for primer and adapter sequences using Tagdust (1.12), (Lassmann et al., 2009).	AR136_rep3_ELT2	bw_0_1_2_4_ce10	GSM1843701_08_AR136_rep3_ELT2.bw
GSM1652677	Larvae_L3	NA	GSE67650		whole worms		 L3	 N2	DPY-27 JL00001  to 1-409 aa.  is the antigen 1-409 aa	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	DPY27 N2 L3 Rep2 ChIPSeq	bd_0_1_2_6_ce10	UsingSRR
GSM1652676	Larvae_L3	NA	GSE67650		whole worms		 L3	 N2	DPY-27 JL00001  to 1-409 aa.  is the antigen 1-409 aa	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	DPY27 N2 L3 Rep1 ChIPSeq	bd_0_1_2_6_ce10	UsingSRR
GSM1186806	Larvae_L3	NA	GSE48917		tra-1(e1834) homozygote L3 stage			 N2	TRA-1 UMN163	ChIP-Seq	ce10	All C. elegans reads were subsequently trimmed to the first 27 bases and aligned to the ce10 reference genome using Bowtie, accepting only uniquely mapped reads with up to two mismatches. For C. briggsae, 48-base reads were aligned using the same Bowtie program settings to the cb4 reference genome.	DZ052_TRA1_tra1homo	bw_0_1_2_4_ce10	GSM1186806_DZ052_TRA1_tra1homo_tr27_ce10_BTm1x200n.bw
GSM1186804	Larvae_L3	NA	GSE48917		tra-1(e1834) heterozygote L3 stage			 N2	TRA-1 UMN163	ChIP-Seq	ce10	All C. elegans reads were subsequently trimmed to the first 27 bases and aligned to the ce10 reference genome using Bowtie, accepting only uniquely mapped reads with up to two mismatches. For C. briggsae, 48-base reads were aligned using the same Bowtie program settings to the cb4 reference genome.	DZ055_TRA1_tra1het	bw_0_1_2_4_ce10	GSM1186804_DZ055_TRA1_tra1het_tr27_ce10_BTm1x200n.bw
GSM1186797	Larvae_L3	NA	GSE48917		N2 strain, L3 stage			 N2	TRA-1 UMN163	ChIP-Seq	ce10	All C. elegans reads were subsequently trimmed to the first 27 bases and aligned to the ce10 reference genome using Bowtie, accepting only uniquely mapped reads with up to two mismatches. For C. briggsae, 48-base reads were aligned using the same Bowtie program settings to the cb4 reference genome.	DZ015_TRA1_N2L3	bw_0_1_2_4_ce10	GSM1186797_DZ015_TRA1_N2L3_tr27_ce10_BTm1x200n.bw
GSM1186795	Larvae_L3	NA	GSE48917		N2 strain, L3 stage			 N2	TRA-1 UMN163	ChIP-Seq	ce10	All C. elegans reads were subsequently trimmed to the first 27 bases and aligned to the ce10 reference genome using Bowtie, accepting only uniquely mapped reads with up to two mismatches. For C. briggsae, 48-base reads were aligned using the same Bowtie program settings to the cb4 reference genome.	DZ012_TRA1_N2L3	bw_0_1_2_4_ce10	GSM1186795_DZ012_TRA1_N2L3_tr27_ce10_BTm1x200n.bw
GSM1200342	Larvae_L3	NA	GSE45678		whole worms		 L3	 N2	KLE-2 SDQ3898  is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	KLE2 N2 L3 Rep4 ChIPSeq	bd_0_1_2_6_ce10	UsingSRR
GSM1200341	Larvae_L3	NA	GSE45678		whole worms		 L3	 N2	KLE-2 SDQ3898  is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	KLE2 N2 L3 Rep3 ChIPSeq	bd_0_1_2_6_ce10	UsingSRR
GSM1200340	Larvae_L3	NA	GSE45678		whole worms		 L3	 N2	KLE-2 SDQ3942  is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	KLE2 N2 L3 Rep2 ChIPSeq	bd_0_1_2_6_ce10	UsingSRR
GSM1200339	Larvae_L3	NA	GSE45678		whole worms		 L3	 N2	KLE-2 SDQ3942  is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http	ChIP-Seq	WS220	Basecalls were performed using CASAVA version 1.8.	KLE2 N2 L3 Rep1 ChIPSeq	bd_0_1_2_6_ce10	UsingSRR
GSM1217520	Larvae_L3	NA	GSE50329		seq-SDQ4663_RPC1_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ4663_RPC1_N2_L3_ChIP	ChIP-Seq	ce10	Worm popcorns were grinded using a mixer mill 400 MM (Retsch) and fixed by 1% formaldehyde for 10 min at room temperature. After quenching the reaction, samples were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) supplemented with protease inhibitors, phosphatase inhibitors and 1% sarkosyl. Using a Bioruptor water-bath sonicator (Diagenode), samples were sonicated at 4 oC with the following settings: ?High? amplitude, 30 sec on/30 sec off, 15 min (including offs). After separating the supernatant from the pellet by centrifugation, the pellet was again sonicated at the same condition but in a half volume of the buffer. Supernatants from the two sonication steps were combined, aliquoted and stored at -80C. For a detailed protocol see http://www.modencode.org/.	seq-SDQ4663_RPC1_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce10	GSM1217520_BC275_peaks.GFF3.gz
GSM1217519	Larvae_L3	NA	GSE50329		seq-SDQ4663_RPC1_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ4663_RPC1_N2_L3_ChIP	ChIP-Seq	ce10	Worm popcorns were grinded using a mixer mill 400 MM (Retsch) and fixed by 1% formaldehyde for 10 min at room temperature. After quenching the reaction, samples were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) supplemented with protease inhibitors, phosphatase inhibitors and 1% sarkosyl. Using a Bioruptor water-bath sonicator (Diagenode), samples were sonicated at 4 oC with the following settings: ?High? amplitude, 30 sec on/30 sec off, 15 min (including offs). After separating the supernatant from the pellet by centrifugation, the pellet was again sonicated at the same condition but in a half volume of the buffer. Supernatants from the two sonication steps were combined, aliquoted and stored at -80C. For a detailed protocol see http://www.modencode.org/.	seq-SDQ4663_RPC1_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce10	GSM1217519_BC058_peaks.GFF3.gz
GSM1217408	Larvae_L3	NA	GSE50301		seq-JL00006_ZFP1_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-JL00006_ZFP1_N2_L3_ChIP	ChIP-Seq	ce10	Worm popcorns were grinded using a mixer mill 400 MM (Retsch) and fixed by 1% formaldehyde for 10 min at room temperature. After quenching the reaction, samples were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) supplemented with protease inhibitors, phosphatase inhibitors and 1% sarkosyl. Using a Bioruptor water-bath sonicator (Diagenode), samples were sonicated at 4 oC with the following settings: ?High? amplitude, 30 sec on/30 sec off, 15 min (including offs). After separating the supernatant from the pellet by centrifugation, the pellet was again sonicated at the same condition but in a half volume of the buffer. Supernatants from the two sonication steps were combined, aliquoted and stored at -80C. For a detailed protocol see http://www.modencode.org/.	seq-JL00006_ZFP1_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce10	GSM1217408_seq-JL00006_ZFP1_N2_L3_2_A_L3E2_BC048_peaks.GFF3.gz
GSM1217407	Larvae_L3	NA	GSE50301		seq-JL00006_ZFP1_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-JL00006_ZFP1_N2_L3_ChIP	ChIP-Seq	ce10	Worm popcorns were grinded using a mixer mill 400 MM (Retsch) and fixed by 1% formaldehyde for 10 min at room temperature. After quenching the reaction, samples were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) supplemented with protease inhibitors, phosphatase inhibitors and 1% sarkosyl. Using a Bioruptor water-bath sonicator (Diagenode), samples were sonicated at 4 oC with the following settings: ?High? amplitude, 30 sec on/30 sec off, 15 min (including offs). After separating the supernatant from the pellet by centrifugation, the pellet was again sonicated at the same condition but in a half volume of the buffer. Supernatants from the two sonication steps were combined, aliquoted and stored at -80C. For a detailed protocol see http://www.modencode.org/.	seq-JL00006_ZFP1_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce10	GSM1217407_seq-JL00006_ZFP1_N2_L3_1_A_L3E1_BC016_peaks.GFF3.gz
GSM1217392	Larvae_L3	NA	GSE50297		seq-SDQ3528_NURF1_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ3528_NURF1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ3528_NURF1_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1217392_SDQ3528_NURF1_L3_ME17_peaks.GFF3.gz
GSM1217391	Larvae_L3	NA	GSE50297		seq-SDQ3528_NURF1_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ3528_NURF1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ3528_NURF1_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1217391_SDQ3528_NURF1_L3_ME16_peaks.GFF3.gz
GSM1217388	Larvae_L3	NA	GSE50296		seq-SDQ3525_NURF1_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ3525_NURF1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ3525_NURF1_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1217388_SDQ3525_NURF1_L3_ME17_peaks.GFF3.gz
GSM1217387	Larvae_L3	NA	GSE50296		seq-SDQ3525_NURF1_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ3525_NURF1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ3525_NURF1_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1217387_SDQ3525_NURF1_L3_ME16_peaks.GFF3.gz
GSM1217384	Larvae_L3	NA	GSE50295		seq-SDQ2940_NURF1_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ2940_NURF1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2940_NURF1_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1217384_SDQ2940_NURF1_L3_ME13_peaks.GFF3.gz
GSM1217383	Larvae_L3	NA	GSE50295		seq-SDQ2940_NURF1_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ2940_NURF1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2940_NURF1_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1217383_SDQ2940_NURF1_L3_ME11_peaks.GFF3.gz
GSM1217380	Larvae_L3	NA	GSE50294		seq-HM4077_LIN61_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-HM4077_LIN61_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-HM4077_LIN61_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1217380_HM4077_LIN61_L3_ME17_peaks.GFF3.gz
GSM1217379	Larvae_L3	NA	GSE50294		seq-HM4077_LIN61_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-HM4077_LIN61_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-HM4077_LIN61_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1217379_HM4077_LIN61_L3_ME11_peaks.GFF3.gz
GSM1217376	Larvae_L3	NA	GSE50293		seq-SDQ2342_LET418_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ2342_LET418_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2342_LET418_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1217376_SDQ2342_LET418_L3_ME8_peaks.GFF3.gz
GSM1217375	Larvae_L3	NA	GSE50293		seq-SDQ2342_LET418_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ2342_LET418_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2342_LET418_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1217375_SDQ2342_LET418_L3_ME7_peaks.GFF3.gz
GSM1217372	Larvae_L3	NA	GSE50292		seq-SDQ3861_LET418_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ3861_LET418_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ3861_LET418_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1217372_SDQ3861_LET418_L3_ME12_peaks.GFF3.gz
GSM1217371	Larvae_L3	NA	GSE50292		seq-SDQ3861_LET418_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ3861_LET418_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ3861_LET418_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1217371_SDQ3861_LET418_L3_ME11_peaks.GFF3.gz
GSM1217368	Larvae_L3	NA	GSE50291		seq-SDQ2354_HDA1_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ2354_HDA1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2354_HDA1_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1217368_SDQ2354_HDA1_L3_ME12_peaks.GFF3.gz
GSM1217367	Larvae_L3	NA	GSE50291		seq-SDQ2354_HDA1_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ2354_HDA1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2354_HDA1_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1217367_SDQ2354_HDA1_L3_ME8_peaks.GFF3.gz
GSM1217234	Larvae_L3	NA	GSE50255		seq-SDQ2370_LIN53_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ2370_LIN53_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2370_LIN53_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1217234_SDQ2370_LIN53_L3_mE02_peaks.GFF3.gz
GSM1217233	Larvae_L3	NA	GSE50255		seq-SDQ2370_LIN53_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ2370_LIN53_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2370_LIN53_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1217233_SDQ2370_LIN53_L3_mE01_peaks.GFF3.gz
GSM1206283	Larvae_L3	NA	GSE49717		seq-JA00001_HTZ1_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-JA00001_HTZ1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-JA00001_HTZ1_N2_L3_ChIP_Rep2	bw_0_1_2_4_ce6	GSM1206283.bigwig
GSM1206282	Larvae_L3	NA	GSE49717		seq-JA00001_HTZ1_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-JA00001_HTZ1_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-JA00001_HTZ1_N2_L3_ChIP_Rep1	bw_0_1_2_4_ce6	GSM1206282.bigwig
GSM1206409	Larvae_L3	NA	GSE49749		seq-SDQ2340_HPL2_N2_L3_ChIP_Rep2		 L3 Larva	 N2	seq-SDQ2340_HPL2_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2340_HPL2_N2_L3_ChIP_Rep2	bd_0_3_4_5_ce6	GSM1206409_SDQ2340_HPL2_L3_ME11_peaks.GFF3.gz
GSM1206408	Larvae_L3	NA	GSE49749		seq-SDQ2340_HPL2_N2_L3_ChIP_Rep1		 L3 Larva	 N2	seq-SDQ2340_HPL2_N2_L3_ChIP	ChIP-Seq	ce6	ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM	seq-SDQ2340_HPL2_N2_L3_ChIP_Rep1	bd_0_3_4_5_ce6	GSM1206408_SDQ2340_HPL2_L3_ME8_peaks.GFF3.gz
GSM1183848	Larvae_L3	NA	GSE48754		NFYA-1_GFP_L3_ChIP_Rep2		 L3	 OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown )	Snyder_NFYA-1_GFP_L3_ChIP	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_NFYA-1_GFP_L3_ChIP_Rep2	bg_0_1_2_4_ce10	GSM1183848_Snyder_NFYA-1_GFP_L3_GFP_rep_2_120213_ROCKFORD_00128_FC63BAJ_L7_CATT.bedgraph.gz
GSM1183846	Larvae_L3	NA	GSE48754		NFYA-1_GFP_L3_ChIP_Rep1		 L3	 OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown )	Snyder_NFYA-1_GFP_L3_ChIP	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_NFYA-1_GFP_L3_ChIP_Rep1	bg_0_1_2_4_ce10	GSM1183846_Snyder_NFYA-1_GFP_L3_GFP_rep_1_120213_ROCKFORD_00128_FC63BAJ_L7_GTAT.bedgraph.gz
GSM1183780	Larvae_L3	NA	GSE48738		NHR-67_GFP_L3_ChIP_Rep2		 L3	 OP373(official name : OP373 genotype : unc119(ed3);wgIs373(nhr-67::TY1 EGFP FLAG;unc119 outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-67 transcription factor. made_by : Bob Waterston's lab from UW )	Snyder_NHR-67_GFP_L3_ChIP	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_NHR-67_GFP_L3_ChIP_Rep2	bg_0_1_2_4_ce10	GSM1183780_Snyder_NHR-67_GFP_L3_GFP_rep_2_111004_MAGNUM_00100_FC64KG3_L4_TGCT.bedgraph.gz
GSM1183778	Larvae_L3	NA	GSE48738		NHR-67_GFP_L3_ChIP_Rep1		 L3	 OP373(official name : OP373 genotype : unc119(ed3);wgIs373(nhr-67::TY1 EGFP FLAG;unc119 outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-67 transcription factor. made_by : Bob Waterston's lab from UW )	Snyder_NHR-67_GFP_L3_ChIP	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_NHR-67_GFP_L3_ChIP_Rep1	bg_0_1_2_4_ce10	GSM1183778_Snyder_NHR-67_GFP_L3_GFP_rep_1_111004_MAGNUM_00100_FC64KG3_L4_ACGT.bedgraph.gz
GSM1183732	Larvae_L3	NA	GSE48726		NHR-11_GFP_L3_ChIP_Rep2		 L3	 OP305(official name : OP305 genotype : unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-11::EGFP fusion protein is expressed in the correct nhr-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-11 transcription factor. made_by : R Waterston )	Snyder_NHR-11_GFP_L3_ChIP	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_NHR-11_GFP_L3_ChIP_Rep2	bg_0_1_2_4_ce10	GSM1183732_Snyder_NHR-11_GFP_L3_GFP_rep_2_110912_COLUMBO_00109_FC631RL_L6_CATT.bedgraph.gz
GSM1183730	Larvae_L3	NA	GSE48726		NHR-11_GFP_L3_ChIP_Rep1		 L3	 OP305(official name : OP305 genotype : unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-11::EGFP fusion protein is expressed in the correct nhr-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-11 transcription factor. made_by : R Waterston )	Snyder_NHR-11_GFP_L3_ChIP	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_NHR-11_GFP_L3_ChIP_Rep1	bg_0_1_2_4_ce10	GSM1183730_Snyder_NHR-11_GFP_L3_GFP_rep_1_110912_COLUMBO_00109_FC631RL_L6_GTAT.bedgraph.gz
GSM1056283	Larvae_L3	NA	GSE43087		 Wild-Type (N2)Wild-type L3s		 L3			GRO-seq	WS230	Libraries were sequenced with Illumina¡¯s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further.	GRO-seq_N2_L3	other	GSM1056283.bigwig
GSM1138439	Larvae_L3	NA	GSE46788		CEH-28 L3 ChIPRep2		 L3	 OP241(official name : OP241 genotype : unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by : Unknwon )	CEH-28 GFP L3 C.elegans ChIP Rep2	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	CEH-28 GFP L3 C.elegans ChIP Rep2	bg_0_1_2_4_ce10	GSM1138439_Snyder_CEH-28_GFP_L3_GFP_rep_2_120316_ROCKFORD_00135_FC64KNR_L4_CATT.bedgraph.gz
GSM1138438	Larvae_L3	NA	GSE46788		CEH-28 L3 ChIPRep1		 L3	 OP241(official name : OP241 genotype : unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by : Unknwon )	CEH-28 GFP L3 C.elegans ChIP Rep1	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	CEH-28 GFP L3 C.elegans ChIP Rep1	bg_0_1_2_4_ce10	GSM1138438_Snyder_CEH-28_GFP_L3_GFP_rep_1_120316_ROCKFORD_00135_FC64KNR_L4_GTAT.bedgraph.gz
GSM1138399	Larvae_L3	NA	GSE46778		NHR-12 L3 ChIPRep2		 L3	 OP318(official name : OP318 genotype : unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross : 3 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by : Bob Waterston's lab from UW )	NHR-12 GFP L3 C.elegans ChIP Rep2	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	NHR-12 GFP L3 C.elegans ChIP Rep2	bg_0_1_2_4_ce10	GSM1138399_Snyder_NHR-12_GFP_L3_GFP_rep_2_120109_MAGNUM_00117_FC64YG1_L7_TGCT.bedgraph.gz
GSM1138398	Larvae_L3	NA	GSE46778		NHR-12 L3 ChIPRep1		 L3	 OP318(official name : OP318 genotype : unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross : 3 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by : Bob Waterston's lab from UW )	NHR-12 GFP L3 C.elegans ChIP Rep1	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	NHR-12 GFP L3 C.elegans ChIP Rep1	bg_0_1_2_4_ce10	GSM1138398_Snyder_NHR-12_GFP_L3_GFP_rep_1_120109_MAGNUM_00117_FC64YG1_L7_ACGT.bedgraph.gz
GSM1138370	Larvae_L3	NA	GSE46771		JUN-1 L3 ChIPRep1		 L3	 OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown )	JUN-1 GFP L3 C.elegans ChIP Rep1	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	JUN-1 GFP L3 C.elegans ChIP Rep1	bg_0_1_2_4_ce10	GSM1138370_Snyder_JUN-1_GFP_L3_GFP_rep_1_111215_SPADE_00129_FC64EJL_L6_ACGT.bedgraph.gz
GSM1138371	Larvae_L3	NA	GSE46771		JUN-1 L3 ChIPRep2		 L3	 OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown )	JUN-1 GFP L3 C.elegans ChIP Rep2	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	JUN-1 GFP L3 C.elegans ChIP Rep2	bg_0_1_2_4_ce10	GSM1138371_Snyder_JUN-1_GFP_L3_GFP_rep_2_111215_SPADE_00129_FC64EJL_L6_TGCT.bedgraph.gz
GSM1138355	Larvae_L3	NA	GSE46767		ZTF-11 L3 ChIPRep2		 L3	 OP236(official name : OP236 genotype : unc119(ed3);wgIs236(elk-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown )	ZTF-11 GFP L3 C.elegans ChIP Rep2	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	ZTF-11 GFP L3 C.elegans ChIP Rep2	bg_0_1_2_4_ce10	GSM1138355_Snyder_ZTF-11_GFP_L3_GFP_rep_2_120105_COLUMBO_00136_FC64YG5_L6_TGCT.bedgraph.gz
GSM1138354	Larvae_L3	NA	GSE46767		ZTF-11 L3 ChIPRep1		 L3	 OP236(official name : OP236 genotype : unc119(ed3);wgIs236(elk-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown )	ZTF-11 GFP L3 C.elegans ChIP Rep1	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	ZTF-11 GFP L3 C.elegans ChIP Rep1	bg_0_1_2_4_ce10	GSM1138354_Snyder_ZTF-11_GFP_L3_GFP_rep_1_120105_COLUMBO_00136_FC64YG5_L6_ACGT.bedgraph.gz
GSM1076676	Larvae_L3	NA	GSE44010		Snyder_ZK377.2_GFP_L3_rep2_GFP_TGCT		 L3	 OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston )	Snyder_ZK377.2_GFP_L3_GFP_TGCT,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_ZK377.2_GFP_L3_rep2_GFP_TGCT	bg_0_1_2_4_ce10	GSM1076676_Snyder_ZK377.2_GFP_L3_rep2-1.bedgraph.gz
GSM1076675	Larvae_L3	NA	GSE44010		Snyder_ZK377.2_GFP_L3_rep1_GFP_ACGT		 L3	 OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston )	Snyder_ZK377.2_GFP_L3_GFP_ACGT,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_ZK377.2_GFP_L3_rep1_GFP_ACGT	bg_0_1_2_4_ce10	GSM1076675_Snyder_ZK377.2_GFP_L3_rep1.bedgraph.gz
GSM1076664	Larvae_L3	NA	GSE44007		Snyder_R02D3.7_GFP_L3_rep2_GFP_ACGT		 L3	 OP218(official name : OP218 genotype : unc-119(ed3); wgIs218(R02D3.7:TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The R02D3.7::EGFP fusion protein is expressed in the correct R02D3.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the RO2D3.7 transcription factor. made_by : Mihail Sarov )	Snyder_R02D3.7_GFP_L3_GFP_ACGT,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_R02D3.7_GFP_L3_rep2_GFP_ACGT	bg_0_1_2_4_ce10	GSM1076664_Snyder_R02D3.7_GFP_L3_rep2.bedgraph.gz
GSM1076663	Larvae_L3	NA	GSE44007		Snyder_R02D3.7_GFP_L3_rep1_GFP_CATT		 L3	 OP218(official name : OP218 genotype : unc-119(ed3); wgIs218(R02D3.7:TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The R02D3.7::EGFP fusion protein is expressed in the correct R02D3.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the RO2D3.7 transcription factor. made_by : Mihail Sarov )	Snyder_R02D3.7_GFP_L3_GFP_CATT,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_R02D3.7_GFP_L3_rep1_GFP_CATT	bg_0_1_2_4_ce10	GSM1076663_Snyder_R02D3.7_GFP_L3_rep1.bedgraph.gz
GSM1005481	Larvae_L3	NA	GSE40945		Snyder_EGL-5_POL-2_L3_rep2		 L3	 OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim )	Snyder EGL-5 POL-2 L3 replicate 2,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder EGL-5 POL-2 L3 replicate 2	bd_0_1_2_6_ce10	UsingSRR
GSM1005480	Larvae_L3	NA	GSE40945		Snyder_EGL-5_POL-2_L3_rep1		 L3	 OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim )	Snyder EGL-5 POL-2 L3 replicate 1,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder EGL-5 POL-2 L3 replicate 1	bd_0_3_4_5_ce10	GSM1005480_Snyder_EGL-5_POL-2_L3_combined_peaks.GFF3.gz
GSM1005477	Larvae_L3	NA	GSE40944		Snyder_EOR-1_POL-2_L3_rep2		 L3	 OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim )	Snyder EOR-1 POL-2 L3 replicate 2,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder EOR-1 POL-2 L3 replicate 2	bd_0_1_2_6_ce10	UsingSRR
GSM1005476	Larvae_L3	NA	GSE40944		Snyder_EOR-1_POL-2_L3_rep1		 L3	 OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim )	Snyder EOR-1 POL-2 L3 replicate 1,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder EOR-1 POL-2 L3 replicate 1	bd_0_3_4_5_ce10	GSM1005476_Snyder_EOR-1_POL-2_L3_combined_peaks.GFF3.gz
GSM929321	Larvae_L3	NA	GSE37881		Snyder_NHR-77_GFP_L3_rep2		 L3	 OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston )	Snyder_NHR-77_GFP_L3 extraction2_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_NHR-77_GFP_L3_rep2 extraction2_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM929320	Larvae_L3	NA	GSE37881		Snyder_NHR-77_GFP_L3_rep1		 L3	 OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston )	Snyder_NHR-77_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_NHR-77_GFP_L3_rep1 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM929305	Larvae_L3	NA	GSE37877		Snyder_FOS-1_GFP_L3_rep2		 L3	 OP304(official name : OP304 genotype : unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by : R Waterston )	Snyder_FOS-1_GFP_L3 extraction2_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_FOS-1_GFP_L3_rep2 extraction2_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM929304	Larvae_L3	NA	GSE37877		Snyder_FOS-1_GFP_L3_rep1		 L3	 OP304(official name : OP304 genotype : unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by : R Waterston )	Snyder_FOS-1_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_FOS-1_GFP_L3_rep1 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM928371	Larvae_L3	NA	GSE37810		Snyder_EOR-1_GFP_L3_rep2		 L3	 OP81(official name : OP81 genotype : unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross : 0 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_EOR-1_GFP_L3 extraction2_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. The sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_EOR-1_GFP_L3_rep2 extraction2_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM928370	Larvae_L3	NA	GSE37810		Snyder_EOR-1_GFP_L3_rep1		 L3	 OP81(official name : OP81 genotype : unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross : 0 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_EOR-1_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. The sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_EOR-1_GFP_L3_rep1 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM928359	Larvae_L3	NA	GSE37807		Snyder_DAF12_GFP_L3_rep2		 L3	 OP167(official name : OP167 genotype : unc119(ed3);wgIs167(daf-12::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by : S Kim )	Snyder_DAF12_GFP_L3 extraction2_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_DAF12_GFP_L3_rep2 extraction2_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM928358	Larvae_L3	NA	GSE37807		Snyder_DAF12_GFP_L3_rep1		 L3	 OP167(official name : OP167 genotype : unc119(ed3);wgIs167(daf-12::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by : S Kim )	Snyder_DAF12_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_DAF12_GFP_L3_rep1 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM928353	Larvae_L3	NA	GSE37806		Snyder_SEA2_GFP_L3_rep2		 L3	 OP193(official name : OP193 genotype : unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The SEA-2::EGFP fusion protein is expressed in the correct sea-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SEA-2 transcription factor. made_by :  )	Snyder_SEA2_GFP_L3 extraction2_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_SEA2_GFP_L3_rep2 extraction2_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM928352	Larvae_L3	NA	GSE37806		Snyder_SEA2_GFP_L3_rep1		 L3	 OP193(official name : OP193 genotype : unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The SEA-2::EGFP fusion protein is expressed in the correct sea-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SEA-2 transcription factor. made_by :  )	Snyder_SEA2_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_SEA2_GFP_L3_rep1 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM864858	Larvae_L3	NA	GSE35277		Snyder_CES1_GFP_L3_rep2		 L3	 OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim )	Snyder_CES1_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_CES1_GFP_L3_rep2 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM864857	Larvae_L3	NA	GSE35277		Snyder_CES1_GFP_L3_rep1		 L3	 OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim )	Snyder_CES1_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS220	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220	Snyder_CES1_GFP_L3_rep1 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM864854	Larvae_L3	NA	GSE35276		Snyder_GEI-11_GFP_L3_rep2		 L3	 OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston )	Snyder_GEI-11_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS190	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS190	Snyder_GEI-11_GFP_L3_rep2 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM864853	Larvae_L3	NA	GSE35276		Snyder_GEI-11_GFP_L3_rep1		 L3	 OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston )	Snyder_GEI-11_GFP_L3 extraction1_seq1 aliquote 1,ChIP DNA	ChIP-Seq	WS190	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS190	Snyder_GEI-11_GFP_L3_rep1 extraction1_seq1 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM779440	Larvae_L3	NA	GSE28777	 whole body	whole body		 L3	 N2	JL00001 DPY27	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-JL00001_DPY27_N2_L3_3	bd_0_3_4_5_ce6	GSM779440_seq-JL00001_DPY27_N2_L3_3_macs14_peaks.gff.gz
GSM779439	Larvae_L3	NA	GSE28777	 whole body	whole body		 L3	 N2	JL00001 DPY27	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-JL00001_DPY27_N2_L3_2	bd_0_3_4_5_ce6	GSM779439_seq-JL00001_DPY27_N2_L3_2_macs14_peaks.gff.gz
GSM727909	Larvae_L3	NA	GSE29427		L3 embyros		 L3	 N2	DPY-27	ChIP-Seq	WS190	Alignment: Sequence reads were mapped to the WS190 reference sequence using BWA	DPY-27	bd_0_1_2_6_ce10	UsingSRR
GSM729391	Larvae_L3	NA	GSE29484		Snyder_NHR-28_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP317(official name : OP317 genotype : unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by : R Waterston )	Snyder_NHR-28_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_NHR-28_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729390	Larvae_L3	NA	GSE29484		Snyder_NHR-28_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP317(official name : OP317 genotype : unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by : R Waterston )	Snyder_NHR-28_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_NHR-28_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729379	Larvae_L3	NA	GSE29481		Snyder_ALY-2_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov )	Snyder_ALY-2_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_ALY-2_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729378	Larvae_L3	NA	GSE29481		Snyder_ALY-2_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov )	Snyder_ALY-2_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_ALY-2_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729375	Larvae_L3	NA	GSE29480		Snyder_DAF-12_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP222(official name : OP222 genotype : unc119(ed3);wgIs222(daf-12:TY1 EGFP FLAG;unc119) outcross : 3 transgene : daf-12 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by : Mihail Sarov )	Snyder_DAF-12_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_DAF-12_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729374	Larvae_L3	NA	GSE29480		Snyder_DAF-12_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP222(official name : OP222 genotype : unc119(ed3);wgIs222(daf-12:TY1 EGFP FLAG;unc119) outcross : 3 transgene : daf-12 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by : Mihail Sarov )	Snyder_DAF-12_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_DAF-12_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729367	Larvae_L3	NA	GSE29478		Snyder_F45C12.2_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP212(official name : OP212 genotype : unc119(ed3);wgIs212(F45C12.2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : F45C12.2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by : Mihail Sarov )	Snyder_F45C12.2_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_F45C12.2_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729366	Larvae_L3	NA	GSE29478		Snyder_F45C12.2_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP212(official name : OP212 genotype : unc119(ed3);wgIs212(F45C12.2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : F45C12.2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by : Mihail Sarov )	Snyder_F45C12.2_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_F45C12.2_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729359	Larvae_L3	NA	GSE29476		Snyder_ZAG-1_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP83(official name : OP83 genotype : unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by : R Waterston )	Snyder_ZAG-1_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_ZAG-1_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729358	Larvae_L3	NA	GSE29476		Snyder_ZAG-1_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP83(official name : OP83 genotype : unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by : R Waterston )	Snyder_ZAG-1_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_ZAG-1_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729347	Larvae_L3	NA	GSE29473		Snyder_EOR-1_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP81(official name : OP81 genotype : unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross : 0 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_EOR-1_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_EOR-1_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729346	Larvae_L3	NA	GSE29473		Snyder_EOR-1_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP81(official name : OP81 genotype : unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross : 0 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_EOR-1_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_EOR-1_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729327	Larvae_L3	NA	GSE29468		Snyder_UNC-62_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim )	Snyder_UNC-62_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_UNC-62_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729326	Larvae_L3	NA	GSE29468		Snyder_UNC-62_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim )	Snyder_UNC-62_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_UNC-62_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729311	Larvae_L3	NA	GSE29464		Snyder_ZTF-4_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP322(official name : ZTF-4 genotype : unc119(ed3);wgIs322(ztf-4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by : Bob Waterston's lab from UW )	Snyder_ZTF-4_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_ZTF-4_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729310	Larvae_L3	NA	GSE29464		Snyder_ZTF-4_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP322(official name : ZTF-4 genotype : unc119(ed3);wgIs322(ztf-4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by : Bob Waterston's lab from UW )	Snyder_ZTF-4_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_ZTF-4_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729299	Larvae_L3	NA	GSE29461		Snyder_PHA-4_GFP_L3_rep2 extraction4_seq4 channel_1		 L3	 OP37(official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_PHA-4_GFP_L3 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_PHA-4_GFP_L3_rep2 extraction4_seq4 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM729298	Larvae_L3	NA	GSE29461		Snyder_PHA-4_GFP_L3_rep1 extraction3_seq3 channel_1		 L3	 OP37(official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_PHA-4_GFP_L3 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_PHA-4_GFP_L3_rep1 extraction3_seq3 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM713175	Larvae_L3	NA	GSE28774	 whole body	whole body		 L3	 N2	SDQ4663_RPC1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ4663_RPC1_N2_MXemb_2_A_EE9_KI031	bd_0_3_4_5_ce6	GSM713175_seq-SDQ4663_RPC1_N2_MXemb_2_A_EE9_KI031_macs14_peaks.gff.gz
GSM713174	Larvae_L3	NA	GSE28774	 whole body	whole body		 L3	 N2	SDQ4663_RPC1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ4663_RPC1_N2_MXemb_1_A_EE8	bd_0_3_4_5_ce6	GSM713174_seq-SDQ4663_RPC1_N2_MXemb_1_A_EE8_macs14_peaks.gff.gz
GSM713173	Larvae_L3	NA	GSE28773	 whole body	whole body		 L3	 N2	SDQ4526 SFC1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ4526_SFC1_N2_MXemb_2_A_EE9_KI035	bd_0_3_4_5_ce6	GSM713173_seq-SDQ4526_SFC1_N2_MXemb_2_A_EE9_KI035_macs14_peaks.gff.gz
GSM713172	Larvae_L3	NA	GSE28773	 whole body	whole body		 L3	 N2	SDQ4526 SFC1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ4526_SFC1_N2_MXemb_1_A_EE8_KI034	bd_0_3_4_5_ce6	GSM713172_seq-SDQ4526_SFC1_N2_MXemb_1_A_EE8_KI034_macs14_peaks.gff.gz
GSM713171	Larvae_L3	NA	GSE28772	 whole body	whole body		 L3	 N2	SDQ4470 TAG315	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ4470_TAG315_N2_MXemb_2_A_EE9_KI033	bd_0_3_4_5_ce6	GSM713171_seq-SDQ4470_TAG315_N2_MXemb_2_A_EE9_KI033_macs14_peaks.gff.gz
GSM713170	Larvae_L3	NA	GSE28772	 whole body	whole body		 L3	 N2	SDQ4470 TAG315	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ4470_TAG315_N2_MXemb_1_A_EE8_KI032	bd_0_3_4_5_ce6	GSM713170_seq-SDQ4470_TAG315_N2_MXemb_1_A_EE8_KI032_macs14_peaks.gff.gz
GSM713150	Larvae_L3	NA	GSE28769	 whole body	whole body		 L3	 N2	SDQ3599 DPL1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ3599_DPL1_N2_L3_2	bd_0_3_4_5_ce6	GSM713150_seq-SDQ3599_DPL1_N2_L3_2_macs14_peaks.gff.gz
GSM713149	Larvae_L3	NA	GSE28769	 whole body	whole body		 L3	 N2	SDQ3599 DPL1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ3599_DPL1_N2_L3_1	bd_0_3_4_5_ce6	GSM713149_seq-SDQ3599_DPL1_N2_L3_1_macs14_peaks.gff.gz
GSM713148	Larvae_L3	NA	GSE28768	 whole body	whole body		 L3	 N2	SDQ3590 EFL1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ3590_EFL1_N2_L3_2	bd_0_3_4_5_ce6	GSM713148_seq-SDQ3590_EFL1_N2_L3_2_macs14_peaks.gff.gz
GSM713147	Larvae_L3	NA	GSE28768	 whole body	whole body		 L3	 N2	SDQ3590 EFL1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ3590_EFL1_N2_L3_1	bd_0_3_4_5_ce6	GSM713147_seq-SDQ3590_EFL1_N2_L3_1_macs14_peaks.gff.gz
GSM713146	Larvae_L3	NA	GSE28767	 whole body	whole body		 L3	 N2	SDQ2370 LIN53	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ2370_LIN53_N2_L3_2	bd_0_3_4_5_ce6	GSM713146_seq-SDQ2370_LIN53_N2_L3_2_macs14_peaks.gff.gz
GSM713145	Larvae_L3	NA	GSE28767	 whole body	whole body		 L3	 N2	SDQ2370 LIN53	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ2370_LIN53_N2_L3_1	bd_0_3_4_5_ce6	GSM713145_seq-SDQ2370_LIN53_N2_L3_1_macs14_peaks.gff.gz
GSM713234	Larvae_L3	NA	GSE28766	 whole body	whole body		 L3	 N2	SDQ0820 EPC1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ0820_EPC1_N2_L3_2_EGS	bd_0_3_4_5_ce6	GSM713234_seq-SDQ0820_EPC1_N2_L3_2_EGS_macs14_peaks.gff.gz
GSM713232	Larvae_L3	NA	GSE28766	 whole body	whole body		 L3	 N2	SDQ0820 EPC1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ0820_EPC1_N2_L3_1_EGS	bd_0_3_4_5_ce6	GSM713232_seq-SDQ0820_EPC1_N2_L3_1_EGS_macs14_peaks.gff.gz
GSM713142	Larvae_L3	NA	GSE28764	 whole body	whole body		 L3	 N2	JL00002 SDC3	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-JL00002_SDC3_N2_L3_3	bd_0_3_4_5_ce6	GSM713142_seq-JL00002_SDC3_N2_L3_3_macs14_peaks.gff.gz
GSM713141	Larvae_L3	NA	GSE28764	 whole body	whole body		 L3	 N2	JL00002 SDC3	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-JL00002_SDC3_N2_L3_2	bd_0_3_4_5_ce6	GSM713141_seq-JL00002_SDC3_N2_L3_2_macs14_peaks.gff.gz
GSM713137	Larvae_L3	NA	GSE28763	 whole body	whole body		 L3	 N2	JA00011 LIN35	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-JA00011_LIN35_N2_L3_4	bd_0_3_4_5_ce6	GSM713137_seq-JA00011_LIN35_N2_L3_4_macs14_peaks.gff.gz
GSM713136	Larvae_L3	NA	GSE28763	 whole body	whole body		 L3	 N2	JA00011 LIN35	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-JA00011_LIN35_N2_L3_2	bd_0_3_4_5_ce6	GSM713136_seq-JA00011_LIN35_N2_L3_2_macs14_peaks.gff.gz
GSM713140	Larvae_L3	NA	GSE28762	 whole body	whole body		 L3	 N2	BK00001 HTZ1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BK00001_HTZ1_N2_L3_1	bd_0_3_4_5_ce6	GSM713140_seq-BK00001_HTZ1_N2_L3_1_macs14_peaks.gff.gz
GSM713139	Larvae_L3	NA	GSE28762	 whole body	whole body		 L3	 N2	JA00001 HTZ1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-JA00001_HTZ1_N2_L3_3	bd_0_3_4_5_ce6	GSM713139_seq-JA00001_HTZ1_N2_L3_3_macs14_peaks.gff.gz
GSM713138	Larvae_L3	NA	GSE28762	 whole body	whole body		 L3	 N2	JA00001 HTZ1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-JA00001_HTZ1_N2_L3_2	bd_0_3_4_5_ce6	GSM713138_seq-JA00001_HTZ1_N2_L3_2_macs14_peaks.gff.gz
GSM712811	Larvae_L3	NA	GSE28761	 whole body	whole body		 L3	 N2	BH00005 LIN9	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BH00005_LIN9_N2_L3_2	bd_0_3_4_5_ce6	GSM712811_seq-BH00005_LIN9_N2_L3_2_macs14_peaks.gff.gz
GSM712810	Larvae_L3	NA	GSE28761	 whole body	whole body		 L3	 N2	BH00005 LIN9	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BH00005_LIN9_N2_L3_1	bd_0_3_4_5_ce6	GSM712810_seq-BH00005_LIN9_N2_L3_1_macs14_peaks.gff.gz
GSM712714	Larvae_L3	NA	GSE28760	 whole body	whole body		 L3	 N2	BH00004_LIN54	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BH00004_LIN54_N2_L3_2	bd_0_3_4_5_ce6	GSM712714_seq-BH00004_LIN54_N2_L3_2_macs14_peaks.gff.gz
GSM712713	Larvae_L3	NA	GSE28760	 whole body	whole body		 L3	 N2	BH00004_LIN54	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BH00004_LIN54_N2_L3_1	bd_0_3_4_5_ce6	GSM712713_seq-BH00004_LIN54_N2_L3_1_macs14_peaks.gff.gz
GSM712712	Larvae_L3	NA	GSE28759	 whole body	whole body		 L3	 N2	BH00003 LIN37	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BH00003_LIN37_N2_L3_2	bd_0_3_4_5_ce6	GSM712712_seq-BH00003_LIN37_N2_L3_2_macs14_peaks.gff.gz
GSM712711	Larvae_L3	NA	GSE28759	 whole body	whole body		 L3	 N2	BH00003 LIN37	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BH00003_LIN37_N2_L3_1	bd_0_3_4_5_ce6	GSM712711_seq-BH00003_LIN37_N2_L3_1_macs14_peaks.gff.gz
GSM712710	Larvae_L3	NA	GSE28758	 whole body	whole body		 L3	 N2	BH00001 LIN52	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BH00001_LIN52_N2_L3_2	bd_0_3_4_5_ce6	GSM712710_seq-BH00001_LIN52_N2_L3_2_macs14_peaks.gff.gz
GSM712709	Larvae_L3	NA	GSE28758	 whole body	whole body		 L3	 N2	BH00001 LIN52	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-BH00001_LIN52_N2_L3_1	bd_0_3_4_5_ce6	GSM712709_seq-BH00001_LIN52_N2_L3_1_macs14_peaks.gff.gz
GSM700190	Larvae_L3	NA	GSE25796		Snyder_EGL-5_GFP_L3_rep2 extraction9_seq9 channel_1		 L3	 OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_EGL-5_GFP_L3 extraction9_seq9 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_EGL-5_GFP_L3_rep2 extraction9_seq9 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM700189	Larvae_L3	NA	GSE25796		Snyder_EGL-5_GFP_L3_rep2 extraction8_seq8 channel_1		 L3	 OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_EGL-5_GFP_L3 extraction8_seq8 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_EGL-5_GFP_L3_rep2 extraction8_seq8 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM700188	Larvae_L3	NA	GSE25796		Snyder_EGL-5_GFP_L3_rep1 extraction7_seq7 channel_1		 L3	 OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_EGL-5_GFP_L3 extraction7_seq7 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_EGL-5_GFP_L3_rep1 extraction7_seq7 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM700187	Larvae_L3	NA	GSE25796		Snyder_EGL-5_GFP_L3_rep1 extraction6_seq6 channel_1		 L3	 OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim )	Snyder_EGL-5_GFP_L3 extraction6_seq6 aliquote 1,channel ch1 is ChIP DNA	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_EGL-5_GFP_L3_rep1 extraction6_seq6 aliquote 1	bd_0_1_2_6_ce10	UsingSRR
GSM677642	Larvae_L3	NA	GSE25792		Snyder_N2_POLII_L3_rep2 extraction2_seq1 channel_2		 L3	 N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 )	POLR2A	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. This method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_N2_POLII_L3_rep2 extraction2_seq1 aliquote 2	bd_0_1_2_6_ce10	UsingSRR
GSM677640	Larvae_L3	NA	GSE25792		Snyder_N2_POLII_L3_rep1 extraction1_seq1 channel_2		 L3	 N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 )	POLR2A	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. This method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_N2_POLII_L3_rep1 extraction1_seq1 aliquote 2	bd_0_1_2_6_ce10	UsingSRR
GSM677602	Larvae_L3	NA	GSE25781		Snyder_MAB5_POLII_L3_rep2 extraction2_seq1 channel_2		 L3	 OP26(made_by : R. Waterston and S. Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs26 [unc-119(+) mab-5::TY1::EGFP::3xFLAG] official name : OP26 )	POLR2A	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. This method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_MAB5_POLII_L3_rep2 extraction2_seq1 aliquote 2	bd_0_1_2_6_ce10	UsingSRR
GSM677600	Larvae_L3	NA	GSE25781		Snyder_MAB5_POLII_L3_rep1 extraction1_seq1 channel_2		 L3	 OP26(made_by : R. Waterston and S. Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs26 [unc-119(+) mab-5::TY1::EGFP::3xFLAG] official name : OP26 )	POLR2A	ChIP-Seq	WS180	Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. This method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180	Snyder_MAB5_POLII_L3_rep1 extraction1_seq1 aliquote 2	bd_0_1_2_6_ce10	UsingSRR
GSM590214	Larvae_L3	NA	GSE20136		L3 XO hermaphrodites		 L3 larval stage	 TY2205		MNase-Seq	WS170	Raw coverage tracks: The sequencing was done using Illumina paired end reads technology. All lanes of each replicate were combined and mapped together. The two single reads of each pair were mapped independently to WS170 genome, using a proprietary software (SeqHit) allowing a single mismatch and no gaps. The hits of the non unique reads were extended to a nucleosomes length and their union defined the non unique regions. The pairs of mapped reads that define a valid (up to 200 basepairs length) and unique regions are collected. The raw coverage of a basepair is caluclated by summing up the number of unique reads covering it. Zero value is assigned to unique basepairs that were covered by none.	XOherm_L3_mononuc_seq	bw_0_1_2_6_ce4	GSM590214.bigwig
GSM435318	Larvae_L3	NA	GSE17458		OP74, HLH-8:GFP:3xFLAG animals		 L3	 OP74	GFP	ChIP-Seq	ce4	Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp.	HLH-8 L3 replicate 2 GFP	bd_0_3_4_5_ce4	GSM435318_Snyder_HLH-8_L3_Rep2_GFP_Peaks.gff3.gz
GSM435316	Larvae_L3	NA	GSE17458		OP74, HLH-8:GFP:3xFLAG animals		 L3	 OP74	GFP	ChIP-Seq	ce4	Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp.	HLH-8 L3 replicate 1 GFP	bd_0_3_4_5_ce4	GSM435316_Snyder_HLH-8_L3_Rep1_GFP_Peaks.gff3.gz
GSM435302	Larvae_L3	NA	GSE17456		OP81, EOR-1:GFP:3xFLAG animals		 L3	 OP81	GFP	ChIP-Seq	ce4	Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp.	EOR-1 L3 replicate 2 GFP	bd_0_3_4_5_ce4	GSM435302_Snyder_EOR-1_L3_Rep2_GFP_Peaks.gff3.gz
GSM435300	Larvae_L3	NA	GSE17456		OP81, EOR-1:GFP:3xFLAG animals		 L3	 OP81	GFP	ChIP-Seq	ce4	Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp.	EOR-1 L3 replicate 1 GFP	bd_0_3_4_5_ce4	GSM435300_Snyder_EOR-1_L3_Rep1_GFP_Peaks.gff3.gz
GSM391228	Larvae_L3	NA	GSE15625		mab-5 transgenic worm OP26		 L3	 OP26	GFP	ChIP-Seq	ce4	Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp.	MAB-5 L3 replicate 2 GFP	bd_0_1_2_5_ce4	GSM391228_Yale_MAB5_L3_GFP_rep2_peaks.bed.gz
GSM391226	Larvae_L3	NA	GSE15625		mab-5 transgenic worm OP26		 L3	 OP26	GFP	ChIP-Seq	ce4	Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp.	MAB-5 L3 replicate 1 GFP	bd_0_1_2_5_ce4	GSM391226_Yale_MAB5_L3_GFP_rep1_peaks.bed.gz
GSM713150	Larvae_L3	NA	GSE28769	 whole body	whole body		 L3	 N2	SDQ3599 DPL1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ3599_DPL1_N2_L3_2	bd_0_3_4_5_ce6	GSM713150_seq-SDQ3599_DPL1_N2_L3_2_macs14_peaks.gff.gz
GSM713149	Larvae_L3	NA	GSE28769	 whole body	whole body		 L3	 N2	SDQ3599 DPL1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ3599_DPL1_N2_L3_1	bd_0_3_4_5_ce6	GSM713149_seq-SDQ3599_DPL1_N2_L3_1_macs14_peaks.gff.gz
GSM713148	Larvae_L3	NA	GSE28768	 whole body	whole body		 L3	 N2	SDQ3590 EFL1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ3590_EFL1_N2_L3_2	bd_0_3_4_5_ce6	GSM713148_seq-SDQ3590_EFL1_N2_L3_2_macs14_peaks.gff.gz
GSM713147	Larvae_L3	NA	GSE28768	 whole body	whole body		 L3	 N2	SDQ3590 EFL1	ChIP-Seq	ce6	BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.	seq-SDQ3590_EFL1_N2_L3_1	bd_0_3_4_5_ce6	GSM713147_seq-SDQ3590_EFL1_N2_L3_1_macs14_peaks.gff.gz