GSM2479976 Embryo_late GSM2479979 GSE94639 whole embryo late C. elegans embryos N2 H3K4me1 ChIP-Seq ce6 Sequences: Standard Illumina software base-calling and quality-control filtering was applied H3K4me1 ChIP-Seq N2 bw_0_1_2_4_ce6 GSM2479976_01_0131_003KManch_N2_H3K4me1_ce6_i73_dmnorm_signal.bw GSM2495722 Embryo_late NA GSE95071 late embryo LIN-54 ChIP-seq in wild-type late embryos Horvitz lab BH0004 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-54 ChIP-seq in wild-type late embryos, rep 1a bd_0_1_2_6_ce10 UsingSRR GSM2495716 Embryo_late NA GSE95071 late embryo LIN-52 ChIP-seq in wild-type late embryos Horvitz lab BH0001 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-52 ChIP-seq in wild-type late embryos, rep 1b bd_0_1_2_6_ce10 UsingSRR GSM2495717 Embryo_late NA GSE95071 late embryo LIN-52 ChIP-seq in wild-type late embryos Horvitz lab BH0001 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-52 ChIP-seq in wild-type late embryos, rep 2b bd_0_1_2_6_ce10 UsingSRR GSM2495706 Embryo_late NA GSE95071 late embryo LIN-9 ChIP-seq in wild-type late embryos Horvitz lab BH0005 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-9 ChIP-seq in wild-type late embryos, rep 1a bd_0_1_2_6_ce10 UsingSRR GSM2495702 Embryo_late NA GSE95071 late embryo LIN-35 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q2003 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-35 ChIP-seq in wild-type late embryos, rep 1a bd_0_1_2_6_ce10 UsingSRR GSM2495697 Embryo_late NA GSE95071 late embryo EFL-1 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q3590 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 EFL-1 ChIP-seq in wild-type late embryos, rep 2b bd_0_1_2_6_ce10 UsingSRR GSM2495696 Embryo_late NA GSE95071 late embryo EFL-1 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q3590 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 EFL-1 ChIP-seq in wild-type late embryos, rep 1b bd_0_1_2_6_ce10 UsingSRR GSM2495690 Embryo_late NA GSE95071 late embryo DPL-1 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q3599 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 DPL-1 ChIP-seq in wild-type late embryos, rep 1b bd_0_1_2_6_ce10 UsingSRR GSM2495723 Embryo_late NA GSE95071 late embryo LIN-54 ChIP-seq in wild-type late embryos Horvitz lab BH0004 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-54 ChIP-seq in wild-type late embryos, rep 2a bd_0_1_2_6_ce10 UsingSRR GSM2495707 Embryo_late NA GSE95071 late embryo LIN-9 ChIP-seq in wild-type late embryos Horvitz lab BH0005 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-9 ChIP-seq in wild-type late embryos, rep 2a bd_0_1_2_6_ce10 UsingSRR GSM2495703 Embryo_late NA GSE95071 late embryo LIN-35 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q2003 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-35 ChIP-seq in wild-type late embryos, rep 2a bd_0_1_2_6_ce10 UsingSRR GSM2495691 Embryo_late NA GSE95071 late embryo DPL-1 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q3599 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 DPL-1 ChIP-seq in wild-type late embryos, rep 2a bd_0_1_2_6_ce10 UsingSRR GSM2495724 Embryo_late NA GSE95071 late embryo LIN-54 ChIP-seq in wild-type late embryos Horvitz lab BH0004 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-54 ChIP-seq in wild-type late embryos, rep 3 bd_0_1_2_6_ce10 UsingSRR GSM2495718 Embryo_late NA GSE95071 late embryo LIN-52 ChIP-seq in wild-type late embryos Horvitz lab BH0001 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-52 ChIP-seq in wild-type late embryos, rep 3 bd_0_1_2_6_ce10 UsingSRR GSM2495712 Embryo_late NA GSE95071 late embryo LIN-37 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q3166 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-37 ChIP-seq in wild-type late embryos, rep 3 bd_0_1_2_6_ce10 UsingSRR GSM2495708 Embryo_late NA GSE95071 late embryo LIN-9 ChIP-seq in wild-type late embryos Horvitz lab BH0005 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 LIN-9 ChIP-seq in wild-type late embryos, rep 3 bd_0_1_2_6_ce10 UsingSRR GSM2495698 Embryo_late NA GSE95071 late embryo EFL-1 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q3590 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 EFL-1 ChIP-seq in wild-type late embryos, rep 3 bd_0_1_2_6_ce10 UsingSRR GSM2495692 Embryo_late NA GSE95071 late embryo DPL-1 ChIP-seq in wild-type late embryos SDIX/Novus Biologicals Q3599 ChIP-Seq ws220 bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10 DPL-1 ChIP-seq in wild-type late embryos, rep 3 bd_0_1_2_6_ce10 UsingSRR GSM1217246 Embryo_late NA GSE50258 seq-SDQ2370_LIN53_N2_LTemb_ChIP_Rep2 Late Embryos N2 seq-SDQ2370_LIN53_N2_LTemb_ChIP ChIP-Seq WS220 Illumina_DNA_Sequencing:JL:1 protocol. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge. Processed data are obtained using following parameters: read length is 36 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2370_LIN53_N2_LTemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217246_seq-SDQ2370_LIN53_N2_LTemb_2_peaks.gff.gz GSM1217245 Embryo_late NA GSE50258 seq-SDQ2370_LIN53_N2_LTemb_ChIP_Rep1 Late Embryos N2 seq-SDQ2370_LIN53_N2_LTemb_ChIP ChIP-Seq WS220 Illumina_DNA_Sequencing:JL:1 protocol. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge. Processed data are obtained using following parameters: read length is 36 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2370_LIN53_N2_LTemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217245_seq-SDQ2370_LIN53_N2_LTemb_1_peaks.gff.gz GSM1183852 Embryo_late NA GSE48755 NFYA-1_GFP_LateEMB_ChIP_Rep2 Late Embryo OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ) Snyder_NFYA-1_GFP_LateEMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NFYA-1_GFP_LateEMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183852_Snyder_NFYA-1_GFP_LateEMB_GFP_rep_2_120213_ROCKFORD_00128_FC63BAJ_L6_TGCT.bedgraph.gz GSM1183850 Embryo_late NA GSE48755 NFYA-1_GFP_LateEMB_ChIP_Rep1 Late Embryo OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ) Snyder_NFYA-1_GFP_LateEMB_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_NFYA-1_GFP_LateEMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183850_Snyder_NFYA-1_GFP_LateEMB_GFP_rep_1_120213_ROCKFORD_00128_FC63BAJ_L6_ACGT.bedgraph.gz GSM1183840 Embryo_late NA GSE48752 HLH-30_GFP_LateEMB_ChIP_Rep2 Late Embryo OP433(official name : OP433 genotype : unc-119(ed3) III; wgIs433(hlh-30::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 description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HLH-30::EGFP fusion protein is expressed in the correct hlh-30 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-30 transcription factor. made_by : Unknown ) Snyder_HLH-30_GFP_LateEMB_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_HLH-30_GFP_LateEMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183840_Snyder_HLH-30_GFP_LateEMB_GFP_rep_2_120228_MAGNUM_00133_FC63B9P_L4_CATT.bedgraph.gz GSM1183838 Embryo_late NA GSE48752 HLH-30_GFP_LateEMB_ChIP_Rep1 Late Embryo OP433(official name : OP433 genotype : unc-119(ed3) III; wgIs433(hlh-30::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 description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HLH-30::EGFP fusion protein is expressed in the correct hlh-30 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-30 transcription factor. made_by : Unknown ) Snyder_HLH-30_GFP_LateEMB_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_HLH-30_GFP_LateEMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183838_Snyder_HLH-30_GFP_LateEMB_GFP_rep_1_120228_MAGNUM_00133_FC63B9P_L4_GTAT.bedgraph.gz GSM1183828 Embryo_late NA GSE48749 DVE-1_GFP_LateEMB_ChIP_Rep2 Late Embryo OP398(official name : OP398 genotype : unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by : Unknown ) Snyder_DVE-1_GFP_LateEMB_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_DVE-1_GFP_LateEMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183828_Snyder_DVE-1_GFP_LateEMB_GFP_rep_2_120302_KOJAK_00083_FC63BAK_L8_CATT.bedgraph.gz GSM1183826 Embryo_late NA GSE48749 DVE-1_GFP_LateEMB_ChIP_Rep1 Late Embryo OP398(official name : OP398 genotype : unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by : Unknown ) Snyder_DVE-1_GFP_LateEMB_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_DVE-1_GFP_LateEMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183826_Snyder_DVE-1_GFP_LateEMB_GFP_rep_1_120302_KOJAK_00083_FC63BAK_L8_GTAT.bedgraph.gz GSM1183772 Embryo_late NA GSE48736 FKH-10_GFP_LEMB_ChIP_Rep2 Late Embryo OP337(official name : OP337 genotype : unc119(ed3);wgIs377(fkh-10::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 FKH-10::EGFP fusion protein is expressed in the correct fkh-10 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FKH-10 transcription factor. made_by : Unknown ) Snyder_FKH-10_GFP_LEMB_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_FKH-10_GFP_LEMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183772_Snyder_FKH-10_GFP_LEMB_GFP_rep_2_111006_MAGNUM_00101_FC64KEN_L8_CATT.bedgraph.gz GSM1183770 Embryo_late NA GSE48736 FKH-10_GFP_LEMB_ChIP_Rep1 Late Embryo OP337(official name : OP337 genotype : unc119(ed3);wgIs377(fkh-10::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 FKH-10::EGFP fusion protein is expressed in the correct fkh-10 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FKH-10 transcription factor. made_by : Unknown ) Snyder_FKH-10_GFP_LEMB_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_FKH-10_GFP_LEMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183770_Snyder_FKH-10_GFP_LEMB_GFP_rep_1_111006_MAGNUM_00101_FC64KEN_L8_GTAT.bedgraph.gz GSM1183760 Embryo_late NA GSE48733 NHR-11_GFP_LEMB_ChIP_Rep2 Late Embryo OP305(official name : OP305 genotype : unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-11::EGFP fusion protein is expressed in the correct nhr-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-11 transcription factor. made_by : R Waterston ) Snyder_NHR-11_GFP_LEMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NHR-11_GFP_LEMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183760_Snyder_NHR-11_GFP_LEMB_GFP_rep_2_110929_COLUMBO_00111_FC64KG6_L3_CATT.bedgraph.gz GSM1183758 Embryo_late NA GSE48733 NHR-11_GFP_LEMB_ChIP_Rep1 Late Embryo OP305(official name : OP305 genotype : unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-11::EGFP fusion protein is expressed in the correct nhr-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-11 transcription factor. made_by : R Waterston ) Snyder_NHR-11_GFP_LEMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NHR-11_GFP_LEMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183758_Snyder_NHR-11_GFP_LEMB_GFP_rep_1_110929_COLUMBO_00111_FC64KG6_L3_GTAT.bedgraph.gz GSM928323 Embryo_late NA GSE37798 Snyder_CEH-26_GFP_LE_rep2 late embryo OP500(official name : OP500 genotype : unc119(ed3);wgIs500(ceh-26::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 Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-26::EGFP fusion protein is expressed in the correct ceh-26 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-26 transcription factor. made_by : R. Waterston ) Snyder_CEH-26_GFP_LE 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_CEH-26_GFP_LE_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928322 Embryo_late NA GSE37798 Snyder_CEH-26_GFP_LE_rep1 late embryo OP500(official name : OP500 genotype : unc119(ed3);wgIs500(ceh-26::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 Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-26::EGFP fusion protein is expressed in the correct ceh-26 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-26 transcription factor. made_by : R. Waterston ) Snyder_CEH-26_GFP_LE extraction1_seq1 aliquote 1,ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_CEH-26_GFP_LE_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM677630 Embryo_late NA GSE25789 Snyder_N2_POLII_lemb_rep2 extraction2_seq1 channel_2 late embryo 20dC 4.5 hrs post-early embryo 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_lemb_rep2 extraction2_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR GSM677628 Embryo_late NA GSE25789 Snyder_N2_POLII_lemb_rep1 extraction1_seq1 channel_2 late embryo 20dC 4.5 hrs post-early embryo 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_lemb_rep1 extraction1_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR