GSM3141759 Larvae_L2 NA GSE114494 L2 larvae N2 H3K4me1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_l2_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141725 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 ATAC-Seq ce10 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_L2_ATAC-seq_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141724 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 ATAC-Seq ce10 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_L2_ATAC-seq_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3142692 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_800U_ml bw_0_1_2_4_ce10 GSM3142692_dnase_wt_l2_rep2_800U_ml.bw GSM3142691 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_400U_ml bw_0_1_2_4_ce10 GSM3142691_dnase_wt_l2_rep2_400U_ml.bw GSM3142690 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_200U_ml bw_0_1_2_4_ce10 GSM3142690_dnase_wt_l2_rep2_200U_ml.bw GSM3142689 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_100U_ml bw_0_1_2_4_ce10 GSM3142689_dnase_wt_l2_rep2_100U_ml.bw GSM3142688 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_50U_ml bw_0_1_2_4_ce10 GSM3142688_dnase_wt_l2_rep2_50U_ml.bw GSM3142686 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_10U_ml bw_0_1_2_4_ce10 GSM3142686_dnase_wt_l2_rep2_10U_ml.bw GSM3142687 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_25U_ml bw_0_1_2_4_ce10 GSM3142687_dnase_wt_l2_rep2_25U_ml.bw GSM3142685 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_5U_ml bw_0_1_2_4_ce10 GSM3142685_dnase_wt_l2_rep2_5U_ml.bw GSM3142684 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep2_2.5U_ml bw_0_1_2_4_ce10 GSM3142684_dnase_wt_l2_rep2_2.5U_ml.bw GSM3142683 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_800U_ml bw_0_1_2_4_ce10 GSM3142683_dnase_wt_l2_rep1_800U_ml.bw GSM3142682 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_400U_ml bw_0_1_2_4_ce10 GSM3142682_dnase_wt_l2_rep1_400U_ml.bw GSM3142681 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_200U_ml bw_0_1_2_4_ce10 GSM3142681_dnase_wt_l2_rep1_200U_ml.bw GSM3142680 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_100U_ml bw_0_1_2_4_ce10 GSM3142680_dnase_wt_l2_rep1_100U_ml.bw GSM3142679 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_50U_ml bw_0_1_2_4_ce10 GSM3142679_dnase_wt_l2_rep1_50U_ml.bw GSM3142678 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_25U_ml bw_0_1_2_4_ce10 GSM3142678_dnase_wt_l2_rep1_25U_ml.bw GSM3142677 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_10U_ml bw_0_1_2_4_ce10 GSM3142677_dnase_wt_l2_rep1_10U_ml.bw GSM3142675 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_2.5U_ml bw_0_1_2_4_ce10 GSM3142675_dnase_wt_l2_rep1_2.5U_ml.bw GSM3142676 Larvae_L2 NA GSE114494 L2 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L2_DNase-seq_rep1_5U_ml bw_0_1_2_4_ce10 GSM3142676_dnase_wt_l2_rep1_5U_ml.bw GSM2730402 Larvae_L2 NA GSE102213 whole worms whole worms L2 GSH100 GFP beads ChIP-Seq ce6 peakcalls performed with cisGenome UNC-55_ChIPSeq bd_0_1_2_non_ce6 GSM2730402_UNC-55_ChIP_peaks.txt.gz GSM2730401 Larvae_L2 NA GSE102213 whole worms whole worms L2 GSH100 GFP beads ChIP-Seq ce6 peakcalls performed with cisGenome UNC-30_ChIPSeq bd_0_1_2_non_ce6 GSM2730401_UNC-30_ChIP_peaks.txt.gz GSM2155063 Larvae_L2 NA GSE81523 whole animal L2 larvae L2 larvae AM1061 POLR2A ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of Pol II in L2 larvae at 34ˇăC, replicate 2 bd_0_1_2_6_ce10 UsingSRR GSM2155062 Larvae_L2 NA GSE81523 whole animal L2 larvae L2 larvae AM1061 POLR2A ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of Pol II in L2 larvae at 34ˇăC, replicate 1 bd_0_1_2_6_ce10 UsingSRR GSM2155061 Larvae_L2 NA GSE81523 whole animal L2 larvae L2 larvae AM1061 POLR2A ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of Pol II in L2 larvae at 20ˇăC, replicate 2 bd_0_1_2_6_ce10 UsingSRR GSM2155060 Larvae_L2 NA GSE81523 whole animal L2 larvae L2 larvae AM1061 POLR2A ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of Pol II in L2 larvae at 20ˇăC, replicate 1 bd_0_1_2_6_ce10 UsingSRR GSM2155059 Larvae_L2 NA GSE81523 whole animal L2 larvae L2 larvae AM1061 HSF-1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of HSF-1 in L2 larvae at 34ˇăC, replicate 2 bd_0_1_2_6_ce10 UsingSRR GSM2155058 Larvae_L2 NA GSE81523 whole animal L2 larvae L2 larvae AM1061 HSF-1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of HSF-1 in L2 larvae at 34ˇăC, replicate 1 bd_0_1_2_6_ce10 UsingSRR GSM2155057 Larvae_L2 NA GSE81523 whole animal L2 larvae L2 larvae AM1061 HSF-1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of HSF-1 in L2 larvae at 20ˇăC, replicate 2 bd_0_1_2_6_ce10 UsingSRR GSM2155056 Larvae_L2 NA GSE81523 whole animal L2 larvae L2 larvae AM1061 HSF-1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of HSF-1 in L2 larvae at 20ˇăC, replicate 1 bd_0_1_2_6_ce10 UsingSRR GSM1186793 Larvae_L2 GSM1186794 GSE48917 N2 strain, L2 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. DZ039_TRA1_N2L2 bw_0_1_2_4_ce10 GSM1186793_DZ039_TRA1_N2L2_tr27_ce10_BTm1x200n.bw GSM1186792 Larvae_L2 GSM1186794 GSE48917 N2 strain, L2 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. DZ038_TRA1_N2L2 bw_0_1_2_4_ce10 GSM1186792_DZ038_TRA1_N2L2_tr27_ce10_BTm1x200n.bw GSM1183812 Larvae_L2 NA GSE48745 MAB-5_GFP_L2_ChIP_Rep2 L2 OP27(official name : OP27 genotype : unc-119(ed3); wgIs27(mab-5::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 and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment 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. made_by : Bob Waterston's lab from UW ) Snyder_MAB-5_GFP_L2_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_MAB-5_GFP_L2_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183812_Snyder_MAB-5_GFP_L2_GFP_rep_2_111031_SPADE_00117_FC64KHE_L8_CATT.bedgraph.gz GSM1183810 Larvae_L2 NA GSE48745 MAB-5_GFP_L2_ChIP_Rep1 L2 OP27(official name : OP27 genotype : unc-119(ed3); wgIs27(mab-5::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 and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment 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. made_by : Bob Waterston's lab from UW ) Snyder_MAB-5_GFP_L2_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_MAB-5_GFP_L2_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183810_Snyder_MAB-5_GFP_L2_GFP_rep_1_120109_ROCKFORD_00117_FC64Y8T_L6_ACGT.bedgraph.gz GSM1183800 Larvae_L2 NA GSE48742 UNC-55_GFP_L2_ChIP_Rep3 L2 NC1639(official name : NC1639 genotype : [wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III outcross : 0 mutagen : None tags : GFP description : Expresses functional *GFP-tagged UNC-55* (COUP-TF) in ventral cord GABA motor neurons (also some ectopic expression in other cells). This line is integrated and shows strong GFP expression. made_by : David Miller lab ) Snyder_UNC-55_GFP_L2_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_UNC-55_GFP_L2_ChIP_Rep3 bg_0_1_2_4_ce10 GSM1183800_Snyder_UNC-55_GFP_L2_GFP_rep_3_110822_COLUMBO_00104_FC64M10_L8_TGCT.bedgraph.gz GSM1183798 Larvae_L2 NA GSE48742 UNC-55_GFP_L2_ChIP_Rep2 L2 NC1639(official name : NC1639 genotype : [wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III outcross : 0 mutagen : None tags : GFP description : Expresses functional *GFP-tagged UNC-55* (COUP-TF) in ventral cord GABA motor neurons (also some ectopic expression in other cells). This line is integrated and shows strong GFP expression. made_by : David Miller lab ) Snyder_UNC-55_GFP_L2_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_UNC-55_GFP_L2_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183798_Snyder_UNC-55_GFP_L2_GFP_rep_2_110822_COLUMBO_00104_FC64M10_L8_ACGT.bedgraph.gz GSM1183796 Larvae_L2 NA GSE48742 UNC-55_GFP_L2_ChIP_Rep1 L2 NC1639(official name : NC1639 genotype : [wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III outcross : 0 mutagen : None tags : GFP description : Expresses functional *GFP-tagged UNC-55* (COUP-TF) in ventral cord GABA motor neurons (also some ectopic expression in other cells). This line is integrated and shows strong GFP expression. made_by : David Miller lab ) Snyder_UNC-55_GFP_L2_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_UNC-55_GFP_L2_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183796_Snyder_UNC-55_GFP_L2_GFP_rep_1_110822_COLUMBO_00104_FC64M10_L8_CATT.bedgraph.gz GSM1183740 Larvae_L2 NA GSE48728 LIN-39_GFP_L2_ChIP_Rep2 L2 OP18(official name : OP18 genotype : unc-119(ed3) III; wgIs18 [unc-119(+) lin-39::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 LIN-39::EGFP fusion protein is expressed in the correct lin-39 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-39 transcription factor. made_by : R. Waterston and S. Kim ) Snyder_LIN-39_GFP_L2_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_LIN-39_GFP_L2_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183740_Snyder_LIN-39_GFP_L2_GFP_rep_2_110915_SPADE_00108_FC631JC_L6_CATT.bedgraph.gz GSM1183738 Larvae_L2 NA GSE48728 LIN-39_GFP_L2_ChIP_Rep1 L2 OP18(official name : OP18 genotype : unc-119(ed3) III; wgIs18 [unc-119(+) lin-39::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 LIN-39::EGFP fusion protein is expressed in the correct lin-39 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-39 transcription factor. made_by : R. Waterston and S. Kim ) Snyder_LIN-39_GFP_L2_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_LIN-39_GFP_L2_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183738_Snyder_LIN-39_GFP_L2_GFP_rep_1_110915_SPADE_00108_FC631JC_L6_GTAT.bedgraph.gz GSM1183640 Larvae_L2 NA GSE48704 SEM-4_GFP_L2_ChIP_Rep2 L2 OP57(official name : OP57 genotype : unc-119(ed3); wgIs57(sem-4::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 and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The SEM-4::EGFP fusion protein is expressed in the correct sem-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sem-4 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_SEM-4_GFP_L2_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. 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_SEM-4_GFP_L2_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183640_Snyder_SEM-4_GFP_L2_rep2.bedgraph.gz GSM1183638 Larvae_L2 NA GSE48704 SEM-4_GFP_L2_ChIP_Rep1 L2 OP57(official name : OP57 genotype : unc-119(ed3); wgIs57(sem-4::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 and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The SEM-4::EGFP fusion protein is expressed in the correct sem-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sem-4 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_SEM-4_GFP_L2_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. 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_SEM-4_GFP_L2_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183638_Snyder_SEM-4_GFP_L2_rep1.bedgraph.gz GSM1183620 Larvae_L2 NA GSE48699 PEB-1_GFP_L2_ChIP_Rep2 L2 OP86(official name : OP86 genotype : unc119(ed3);wgIs86(peb-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 PEB-1::EGFP fusion protein is expressed in the correct peb-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PEB-1 transcription factor. made_by : R Waterston ) Snyder_PEB-1_GFP_L2_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. 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_PEB-1_GFP_L2_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183620_Snyder_PEB-1_GFP_L2_rep2.bedgraph.gz GSM1183618 Larvae_L2 NA GSE48699 PEB-1_GFP_L2_ChIP_Rep1 L2 OP86(official name : OP86 genotype : unc119(ed3);wgIs86(peb-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 PEB-1::EGFP fusion protein is expressed in the correct peb-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PEB-1 transcription factor. made_by : R Waterston ) Snyder_PEB-1_GFP_L2_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. 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_PEB-1_GFP_L2_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183618_Snyder_PEB-1_GFP_L2_rep1.bedgraph.gz GSM1138443 Larvae_L2 NA GSE46789 LSY-2 L2 v2 ChIPRep2 L2 OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-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 LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ) LSY-2 GFP L2 v2 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 LSY-2 GFP L2 v2 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138443_Snyder_LSY-2_GFP_L2_GFP_rep_2_120306_COLUMBO_00154_FC64V9L_L3_CATT.bedgraph.gz GSM1138442 Larvae_L2 NA GSE46789 LSY-2 L2 v2 ChIPRep1 L2 OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-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 LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ) LSY-2 GFP L2 v2 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 LSY-2 GFP L2 v2 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138442_Snyder_LSY-2_GFP_L2_GFP_rep_1_120306_COLUMBO_00154_FC64V9L_L3_GTAT.bedgraph.gz GSM1138423 Larvae_L2 NA GSE46784 NHR-21 L2 ChIPRep2 L2 OP361(official name : OP361 genotype : unc119(ed3);wgIs361(nhr-21::TY1-GFP-3xFLAG;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-21::EGFP fusion protein is expressed in the correct nhr-21 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-21 transcription factor. made_by : Unknown ) NHR-21 GFP L2 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 NHR-21 GFP L2 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138423_Snyder_NHR-21_GFP_L2_GFP_rep_2_120302_COLUMBO_00153_FC63BFU_L3_TGCT.bedgraph.gz GSM1138422 Larvae_L2 NA GSE46784 NHR-21 L2 ChIPRep1 L2 OP361(official name : OP361 genotype : unc119(ed3);wgIs361(nhr-21::TY1-GFP-3xFLAG;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-21::EGFP fusion protein is expressed in the correct nhr-21 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-21 transcription factor. made_by : Unknown ) NHR-21 GFP L2 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 NHR-21 GFP L2 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138422_Snyder_NHR-21_GFP_L2_GFP_rep_1_120302_COLUMBO_00153_FC63BFU_L3_ACGT.bedgraph.gz GSM1138419 Larvae_L2 NA GSE46783 ZTF-4 L2 ChIPRep2 L2 OP322(official name : OP322 genotype : unc-119(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 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 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 ) ZTF-4 GFP L2 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-4 GFP L2 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138419_Snyder_ZTF-4_GFP_L2_GFP_rep_2_120224_MAGNUM_00132_FC63BBD_L4_TGCT.bedgraph.gz GSM1138418 Larvae_L2 NA GSE46783 ZTF-4 L2 ChIPRep1 L2 OP322(official name : OP322 genotype : unc-119(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 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 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 ) ZTF-4 GFP L2 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-4 GFP L2 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138418_Snyder_ZTF-4_GFP_L2_GFP_rep_1_120224_MAGNUM_00132_FC63BBD_L4_ACGT.bedgraph.gz GSM1138411 Larvae_L2 NA GSE46781 LIN-13 L2 ChIPRep2 L2 OP49(official name : OP49 genotype : unc119(ed3);wgIs49(lin-13::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 LIN-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by : Unknown ) LIN-13 GFP L2 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 LIN-13 GFP L2 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138411_Snyder_LIN-13_GFP_L2_GFP_rep_2_120223_SPADE_00141_FC63BFT_L6_TGCT.bedgraph.gz GSM1138410 Larvae_L2 NA GSE46781 LIN-13 L2 ChIPRep1 L2 OP49(official name : OP49 genotype : unc119(ed3);wgIs49(lin-13::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 LIN-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by : Unknown ) LIN-13 GFP L2 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 LIN-13 GFP L2 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138410_Snyder_LIN-13_GFP_L2_GFP_rep_1_120223_SPADE_00141_FC63BFT_L6_ACGT.bedgraph.gz GSM1138391 Larvae_L2 NA GSE46776 UNC-39 L2 ChIPRep2 L2 OP186(official name : OP186 genotype : unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;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-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by : Unknown ) UNC-39 GFP L2 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 UNC-39 GFP L2 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138391_Snyder_UNC-39_GFP_L2_GFP_rep_2_111129_COLUMBO_00128_FC6376J_L4_CATT.bedgraph.gz GSM1138390 Larvae_L2 NA GSE46776 UNC-39 L2 ChIPRep1 L2 OP186(official name : OP186 genotype : unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;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-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by : Unknown ) UNC-39 GFP L2 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 UNC-39 GFP L2 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138390_Snyder_UNC-39_GFP_L2_GFP_rep_1_111129_COLUMBO_00128_FC6376J_L4_GTAT.bedgraph.gz GSM1138383 Larvae_L2 NA GSE46774 nhr-23 L2 ChIPRep2 L2 OP43(official name : OP43 genotype : unc-119(ed3); wgIs43(nhr-23::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 and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The NHR-23::EGFP fusion protein is expressed in the correct nhr-23 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-223 transcription factor. made_by : Bob Waterston's lab from UW ) nhr-23 GFP L2 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 nhr-23 GFP L2 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138383_Snyder_nhr-23_GFP_L2_GFP_rep_2_111117_SPADE_00122_FC63773_L3_TGCT.bedgraph.gz GSM1138382 Larvae_L2 NA GSE46774 nhr-23 L2 ChIPRep1 L2 OP43(official name : OP43 genotype : unc-119(ed3); wgIs43(nhr-23::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 and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The NHR-23::EGFP fusion protein is expressed in the correct nhr-23 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-223 transcription factor. made_by : Bob Waterston's lab from UW ) nhr-23 GFP L2 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 nhr-23 GFP L2 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138382_Snyder_nhr-23_GFP_L2_GFP_rep_1_111117_SPADE_00122_FC63773_L3_ACGT.bedgraph.gz GSM1138379 Larvae_L2 NA GSE46773 ELT-1 L2 ChIPRep2 L2 OP354(official name : OP354 genotype : unc119(ed3);wgIs354(elt-1::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 bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ) ELT-1 GFP L2 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 ELT-1 GFP L2 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138379_Snyder_ELT-1_GFP_L2_GFP_rep_2_111110_KOJAK_00069_FC64FPY_L8_TGCT.bedgraph.gz GSM1138378 Larvae_L2 NA GSE46773 ELT-1 L2 ChIPRep1 L2 OP354(official name : OP354 genotype : unc119(ed3);wgIs354(elt-1::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 bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ) ELT-1 GFP L2 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 ELT-1 GFP L2 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138378_Snyder_ELT-1_GFP_L2_GFP_rep_1_111110_KOJAK_00069_FC64FPY_L8_ACGT.bedgraph.gz GSM1076660 Larvae_L2 NA GSE44006 Snyder_ALY-2_GFP_L2_rep2_CATT L2 OP217(official name : OP217 genotype : unc-119(ed3); wgIs217(aly-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 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_L2_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_ALY-2_GFP_L2_rep2_CATT bg_0_1_2_4_ce10 GSM1076660_Snyder_ALY-2_GFP_L2_rep2-1.bedgraph.gz GSM1076659 Larvae_L2 NA GSE44006 Snyder_ALY-2_GFP_L2_rep1_GTAT L2 OP217(official name : OP217 genotype : unc-119(ed3); wgIs217(aly-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 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_L2_GTAT,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_ALY-2_GFP_L2_rep1_GTAT bg_0_1_2_4_ce10 GSM1076659_Snyder_ALY-2_GFP_L2_rep1.bedgraph.gz GSM1076656 Larvae_L2 NA GSE44005 Snyder_F45C12.2_GFP_L2_rep2_TGCT L2 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_L2_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. 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_F45C12.2_GFP_L2_rep2_TGCT bg_0_1_2_4_ce10 GSM1076656_Snyder_F45C12.2_GFP_L2_rep2-1.bedgraph.gz GSM1076655 Larvae_L2 NA GSE44005 Snyder_F45C12.2_GFP_L2_rep1_ACGT L2 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_L2_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_F45C12.2_GFP_L2_rep1_ACGT bg_0_1_2_4_ce10 GSM1076655_Snyder_F45C12.2_GFP_L2_rep1-1.bedgraph.gz GSM929329 Larvae_L2 NA GSE37883 Snyder_NHR-116_GFP_L2_rep2 L2 OP226(official name : OP226 genotype : unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-116 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-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by : M Sarov ) Snyder_NHR-116_GFP_L2 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-116_GFP_L2_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929328 Larvae_L2 NA GSE37883 Snyder_NHR-116_GFP_L2_rep1 L2 OP226(official name : OP226 genotype : unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-116 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-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by : M Sarov ) Snyder_NHR-116_GFP_L2 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_NHR-116_GFP_L2_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929317 Larvae_L2 NA GSE37880 Snyder_NHR-77_GFP_L2_rep2 L2 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_L2 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. 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_L2_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929316 Larvae_L2 NA GSE37880 Snyder_NHR-77_GFP_L2_rep1 L2 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_L2 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_NHR-77_GFP_L2_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929313 Larvae_L2 NA GSE37879 Snyder_ZK377.2_GFP_L2_rep2 L2 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_L2 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_ZK377.2_GFP_L2_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929312 Larvae_L2 NA GSE37879 Snyder_ZK377.2_GFP_L2_rep1 L2 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_L2 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_ZK377.2_GFP_L2_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928367 Larvae_L2 NA GSE37809 Snyder_GEI-11_GFP_L2_rep2 L2 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_L2 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_GEI-11_GFP_L2_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928366 Larvae_L2 NA GSE37809 Snyder_GEI-11_GFP_L2_rep1 L2 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_L2 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. 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_GEI-11_GFP_L2_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928351 Larvae_L2 NA GSE37805 Snyder_NHR11_GFP_L2_rep2 L2 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_NHR11_GFP_L2 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_NHR11_GFP_L2_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928350 Larvae_L2 NA GSE37805 Snyder_NHR11_GFP_L2_rep1 L2 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_NHR11_GFP_L2 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. 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_NHR11_GFP_L2_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729387 Larvae_L2 NA GSE29483 Snyder_R02D3.7_GFP_L2_rep2 extraction4_seq4 channel_1 L2 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 : ) Snyder_R02D3.7_GFP_L2 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_R02D3.7_GFP_L2_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729386 Larvae_L2 NA GSE29483 Snyder_R02D3.7_GFP_L2_rep1 extraction3_seq3 channel_1 L2 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 : ) Snyder_R02D3.7_GFP_L2 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_R02D3.7_GFP_L2_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729351 Larvae_L2 NA GSE29474 Snyder_NHR-6v2_GFP_L2_rep2 extraction4_seq4 channel_1 L2 OP90(official name : OP90 genotype : unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG] 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 NHR-6::EGFP fusion protein is expressed in neurons surrounding pharynx at L2 stage. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-6 transcription factor. made_by : R. Waterston ) Snyder_NHR-6v2_GFP_L2 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_NHR-6v2_GFP_L2_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729350 Larvae_L2 NA GSE29474 Snyder_NHR-6v2_GFP_L2_rep1 extraction3_seq3 channel_1 L2 OP90(official name : OP90 genotype : unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG] 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 NHR-6::EGFP fusion protein is expressed in neurons surrounding pharynx at L2 stage. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-6 transcription factor. made_by : R. Waterston ) Snyder_NHR-6v2_GFP_L2 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_NHR-6v2_GFP_L2_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729343 Larvae_L2 NA GSE29472 Snyder_C01B12.2_GFP_L2_rep2 extraction4_seq4 channel_1 L2 OP343(official name : OP343 genotype : unc119(ed3);wgIs343(C01B12.2: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 bombardment transformation of an unc-119(ed3) strain. The C01B12.2::EGFP fusion protein has broad expression pattern at L2 stage. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_C01B12.2_GFP_L2 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_C01B12.2_GFP_L2_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729342 Larvae_L2 NA GSE29472 Snyder_C01B12.2_GFP_L2_rep1 extraction3_seq3 channel_1 L2 OP343(official name : OP343 genotype : unc119(ed3);wgIs343(C01B12.2: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 bombardment transformation of an unc-119(ed3) strain. The C01B12.2::EGFP fusion protein has broad expression pattern at L2 stage. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_C01B12.2_GFP_L2 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_C01B12.2_GFP_L2_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729339 Larvae_L2 NA GSE29471 Snyder_UNC-62_GFP_L2_rep2 extraction4_seq4 channel_1 L2 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_L2 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_L2_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729338 Larvae_L2 NA GSE29471 Snyder_UNC-62_GFP_L2_rep1 extraction3_seq3 channel_1 L2 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_L2 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_L2_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729335 Larvae_L2 NA GSE29470 Snyder_FOS-1_GFP_L2_rep2 extraction4_seq4 channel_1 L2 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_L2 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_FOS-1_GFP_L2_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729334 Larvae_L2 NA GSE29470 Snyder_FOS-1_GFP_L2_rep1 extraction3_seq3 channel_1 L2 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_L2 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_FOS-1_GFP_L2_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729319 Larvae_L2 NA GSE29466 Snyder_ZAG-1_GFP_L2_rep2 extraction4_seq4 channel_1 L2 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_L2 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_ZAG-1_GFP_L2_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729318 Larvae_L2 NA GSE29466 Snyder_ZAG-1_GFP_L2_rep1 extraction3_seq3 channel_1 L2 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_L2 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_L2_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700179 Larvae_L2 NA GSE26153 Snyder_PHA-4_GFP_L2_rep1 extraction3_seq3 channel_1 L2 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_L2 extraction3_seq3 aliquote 1,channel ch1 is 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. 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 WS190 Snyder_PHA-4_GFP_L2_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700178 Larvae_L2 NA GSE26153 Snyder_PHA-4_GFP_L2_rep2 extraction2_seq2 channel_1 L2 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_L2 extraction2_seq2 aliquote 1,channel ch1 is 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_PHA-4_GFP_L2_rep2 extraction2_seq2 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700177 Larvae_L2 NA GSE26153 Snyder_PHA-4_GFP_L2_rep2 extraction1_seq1 channel_1 L2 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_L2 extraction1_seq1 aliquote 1,channel ch1 is 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_PHA-4_GFP_L2_rep2 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700165 Larvae_L2 NA GSE25787 Snyder_ALR-1_GFP_L2_rep1 extraction3_seq3 channel_1 L2 OP200(official name : OP200 genotype : unc119(ed3);wgIs200(alr-1::TY1 EGFP FLAG C;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : his 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 ALR-1::EGFP fusion protein is expressed in the correct alr-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALR-1 transcription factor. made_by : R. Waterston ) Snyder_ALR-1_GFP_L2 extraction3_seq3 aliquote 1,channel ch1 is 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_ALR-1_GFP_L2_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700164 Larvae_L2 NA GSE25787 Snyder_ALR-1_GFP_L2_rep1 extraction2_seq2 channel_1 L2 OP200(official name : OP200 genotype : unc119(ed3);wgIs200(alr-1::TY1 EGFP FLAG C;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : his 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 ALR-1::EGFP fusion protein is expressed in the correct alr-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALR-1 transcription factor. made_by : R. Waterston ) Snyder_ALR-1_GFP_L2 extraction2_seq2 aliquote 1,channel ch1 is 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_ALR-1_GFP_L2_rep1 extraction2_seq2 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700163 Larvae_L2 NA GSE25787 Snyder_ALR-1_GFP_L2_rep2 extraction1_seq1 channel_1 L2 OP200(official name : OP200 genotype : unc119(ed3);wgIs200(alr-1::TY1 EGFP FLAG C;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : his 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 ALR-1::EGFP fusion protein is expressed in the correct alr-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALR-1 transcription factor. made_by : R. Waterston ) Snyder_ALR-1_GFP_L2 extraction1_seq1 aliquote 1,channel ch1 is 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_ALR-1_GFP_L2_rep2 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM677638 Larvae_L2 NA GSE25791 Snyder_N2_POLII_L2_rep2 extraction2_seq1 channel_2 L2 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_L2_rep2 extraction2_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR GSM677636 Larvae_L2 NA GSE25791 Snyder_N2_POLII_L2_rep1 extraction1_seq1 channel_2 L2 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_L2_rep1 extraction1_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR