GSM3141757 Larvae_L1 NA GSE114494 L1 larvae N2 H3K4me1 ChIP-Seq cel2 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_l1_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141756 Larvae_L1 NA GSE114494 L1 larvae N2 H3K4me1 ChIP-Seq cel2 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_l1_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3141723 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 ATAC-Seq cel2 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_L1_ATAC-seq_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141722 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 ATAC-Seq cel2 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_L1_ATAC-seq_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3142674 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_800U_ml bw_0_1_2_4_ce10 GSM3142674_dnase_wt_l1_rep2_800U_ml.bw GSM3142673 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_400U_ml bw_0_1_2_4_ce10 GSM3142673_dnase_wt_l1_rep2_400U_ml.bw GSM3142672 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_200U_ml bw_0_1_2_4_ce10 GSM3142672_dnase_wt_l1_rep2_200U_ml.bw GSM3142671 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_100U_ml bw_0_1_2_4_ce10 GSM3142671_dnase_wt_l1_rep2_100U_ml.bw GSM3142670 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_50U_ml bw_0_1_2_4_ce10 GSM3142670_dnase_wt_l1_rep2_50U_ml.bw GSM3142669 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_25U_ml bw_0_1_2_4_ce10 GSM3142669_dnase_wt_l1_rep2_25U_ml.bw GSM3142668 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_10U_ml bw_0_1_2_4_ce10 GSM3142668_dnase_wt_l1_rep2_10U_ml.bw GSM3142667 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_5U_ml bw_0_1_2_4_ce10 GSM3142667_dnase_wt_l1_rep2_5U_ml.bw GSM3142666 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep2_2.5U_ml bw_0_1_2_4_ce10 GSM3142666_dnase_wt_l1_rep2_2.5U_ml.bw GSM3142665 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_800U_ml bw_0_1_2_4_ce10 GSM3142665_dnase_wt_l1_rep1_800U_ml.bw GSM3142664 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_400U_ml bw_0_1_2_4_ce10 GSM3142664_dnase_wt_l1_rep1_400U_ml.bw GSM3142663 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_200U_ml bw_0_1_2_4_ce10 GSM3142663_dnase_wt_l1_rep1_200U_ml.bw GSM3142662 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_100U_ml bw_0_1_2_4_ce10 GSM3142662_dnase_wt_l1_rep1_100U_ml.bw GSM3142661 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_50U_ml bw_0_1_2_4_ce10 GSM3142661_dnase_wt_l1_rep1_50U_ml.bw GSM3142660 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_25U_ml bw_0_1_2_4_ce10 GSM3142660_dnase_wt_l1_rep1_25U_ml.bw GSM3142659 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_10U_ml bw_0_1_2_4_ce10 GSM3142659_dnase_wt_l1_rep1_10U_ml.bw GSM3142658 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_5U_ml bw_0_1_2_4_ce10 GSM3142658_dnase_wt_l1_rep1_5U_ml.bw GSM3142657 Larvae_L1 NA GSE114494 L1 larvae wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L1_DNase-seq_rep1_2.5U_ml bw_0_1_2_4_ce10 GSM3142657_dnase_wt_l1_rep1_2.5U_ml.bw GSM2690484 Larvae_L1 NA GSE100651 Sorted L1 PGCs Starved L1 ATAC-Seq ce10 Base calling and demultiplexing was performed at UC reverside IIGB Genomics Core facility with CASAVA 1.8. nos-1(gv5) nos-2(RNAi) ATAC-seq (Replicate) bd_0_1_2_6_ce10 UsingSRR GSM2690483 Larvae_L1 NA GSE100651 Sorted L1 PGCs Starved L1 ATAC-Seq ce10 Base calling and demultiplexing was performed at UC reverside IIGB Genomics Core facility with CASAVA 1.8. nos-1(gv5) nos-2(RNAi) ATAC-seq bd_0_1_2_6_ce10 UsingSRR GSM2690482 Larvae_L1 NA GSE100651 Sorted L1 PGCs Starved L1 ATAC-Seq ce10 Base calling and demultiplexing was performed at UC reverside IIGB Genomics Core facility with CASAVA 1.8. Wild-type ATAC-seq (Replicate) bg_0_1_2_4_ce10 GSM2690482_nanos-dependent_ATACseq_peak_treat_pileup.bedgraph.gz GSM2690481 Larvae_L1 NA GSE100651 Sorted L1 PGCs Starved L1 ATAC-Seq ce10 Base calling and demultiplexing was performed at UC reverside IIGB Genomics Core facility with CASAVA 1.8. Wild-type ATAC-seq bd_0_1_2_7_ce10 GSM2690481_nanos-dependent_ATACseq_peak.xls.gz GSM2564326 Larvae_L1 NA GSE97425 N2 L1 Arrest L1 Arrest N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 L1 Arrest Dnase-seq Biological Replicate V bw_0_1_2_4_ce10 GSM2564326_merged.L1.ce10.V.total.bw GSM2564325 Larvae_L1 NA GSE97425 N2 L1 Arrest L1 Arrest N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 L1 Arrest Dnase-seq Biological Replicate W bw_0_1_2_4_ce10 GSM2564325_merged.L1.ce10.W.total.bw GSM2564324 Larvae_L1 NA GSE97425 N2 L1 Arrest L1 Arrest N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 L1 Arrest Dnase-seq Biological Replicate X bw_0_1_2_4_ce10 GSM2564324_merged.L1.ce10.X.total.bw GSM2564323 Larvae_L1 NA GSE97425 N2 L1 Arrest L1 Arrest N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 L1 Arrest Dnase-seq Biological Replicate Y bw_0_1_2_4_ce10 GSM2564323_merged.L1.ce10.Y.total.bw GSM2564322 Larvae_L1 NA GSE97425 N2 L1 Arrest L1 Arrest N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 L1 Arrest Dnase-seq Biological Replicate Z bw_0_1_2_4_ce10 GSM2564322_merged.L1.ce10.Z.negative.bw GSM1089227 Larvae_L1 NA GSE44710 embryonic stage Fed L1 N2 PHA-4 ChIP-Seq WS232 Basecalls performed using CASAVA version 1.7 PHA-4 ChIP repA bg_0_1_2_4_ce10 GSM1089227_N2_pha4_A_macs2_treat_pileup.bedgraph.gz GSM1089224 Larvae_L1 NA GSE44710 embryonic stage Fed L1 N2 NHR-25 ChIP-Seq WS232 Basecalls performed using CASAVA version 1.7 NHR-25 ChIP repB bg_0_1_2_4_ce10 GSM1089224_N2_nhr25_B_macs2_treat_pileup.bedgraph.gz GSM1089223 Larvae_L1 NA GSE44710 embryonic stage Fed L1 N2 NHR-25 ChIP-Seq WS232 Basecalls performed using CASAVA version 1.7 NHR-25 ChIP repA bg_0_1_2_4_ce10 GSM1089223_N2_nhr25_A_macs2_treat_pileup.bedgraph.gz GSM1183784 Larvae_L1 NA GSE48739 LIN-39_GFP_L1_ChIP_Rep2 fed L1 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_L1_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_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183784_Snyder_LIN-39_GFP_L1_GFP_rep_2_110829_COLUMBO_00106_FC631M9_L4_CATT.bedgraph.gz GSM1183782 Larvae_L1 NA GSE48739 LIN-39_GFP_L1_ChIP_Rep1 fed L1 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_L1_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_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183782_Snyder_LIN-39_GFP_L1_GFP_rep_1_110829_COLUMBO_00106_FC631M9_L4_GTAT.bedgraph.gz GSM1183768 Larvae_L1 NA GSE48735 NHR-28_GFP_L1_ChIP_Rep2 L1 26dC OP317(official name : OP317 genotype : unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by : R Waterston ) Snyder_NHR-28_GFP_L1_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-28_GFP_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183768_Snyder_NHR-28_GFP_L1_GFP_rep_2_110929_COLUMBO_00111_FC64KG6_L4_TGCT.bedgraph.gz GSM1183766 Larvae_L1 NA GSE48735 NHR-28_GFP_L1_ChIP_Rep1 L1 26dC OP317(official name : OP317 genotype : unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by : R Waterston ) Snyder_NHR-28_GFP_L1_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-28_GFP_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183766_Snyder_NHR-28_GFP_L1_GFP_rep_1_110929_COLUMBO_00111_FC64KG6_L4_ACGT.bedgraph.gz GSM1183764 Larvae_L1 NA GSE48734 NHR-11_GFP_L1_ChIP_Rep2 L1 26dC 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_L1_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_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183764_Snyder_NHR-11_GFP_L1_GFP_rep_2_110929_COLUMBO_00111_FC64KG6_L3_TGCT.bedgraph.gz GSM1183762 Larvae_L1 NA GSE48734 NHR-11_GFP_L1_ChIP_Rep1 L1 26dC 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_L1_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_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183762_Snyder_NHR-11_GFP_L1_GFP_rep_1_110929_COLUMBO_00111_FC64KG6_L3_ACGT.bedgraph.gz GSM1183708 Larvae_L1 NA GSE48720 nhr-237_GFP_L1_ChIP_Rep2 L1 26dC OP228(official name : OP228 genotype : unc119(ed3);wgIs228(nhr-237: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-237::EGFP fusion protein is expressed in the correct nhr-237 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-237 transcription factor. made_by : Unknown ) Snyder_nhr-237_GFP_L1_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 WS180 Snyder_nhr-237_GFP_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183708_Snyder_nhr-237_GFP_L1_rep2-1.bedgraph.gz GSM1183706 Larvae_L1 NA GSE48720 nhr-237_GFP_L1_ChIP_Rep1 L1 26dC OP228(official name : OP228 genotype : unc119(ed3);wgIs228(nhr-237: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-237::EGFP fusion protein is expressed in the correct nhr-237 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-237 transcription factor. made_by : Unknown ) Snyder_nhr-237_GFP_L1_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. 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-237_GFP_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183706_Snyder_nhr-237_GFP_L1_rep1-1.bedgraph.gz GSM1183695 Larvae_L1 NA GSE48717 LSY-2_GFP_Starved_Input_Rep2 L1 larva DevStageWorm:starved L1:MS:1(official name : starved L1 ) 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_LSY-2_GFP_Starved_Input_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1183696 Larvae_L1 NA GSE48717 LSY-2_GFP_Starved_ChIP_Rep2 L1 larva DevStageWorm:starved L1:MS:1(official name : starved L1 ) Snyder_LSY-2_GFP_Starved_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_LSY-2_GFP_Starved_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183696_Snyder_LSY-2_GFP_Starved_L1_rep2-1.bedgraph.gz GSM1183694 Larvae_L1 NA GSE48717 LSY-2_GFP_Starved_ChIP_Rep1 L1 larva DevStageWorm:starved L1:MS:1(official name : starved L1 ) Snyder_LSY-2_GFP_Starved_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. 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_LSY-2_GFP_Starved_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183694_Snyder_LSY-2_GFP_Starved_L1_rep1.bedgraph.gz GSM1183693 Larvae_L1 NA GSE48717 LSY-2_GFP_Starved_Input_Rep1 L1 larva DevStageWorm:starved L1:MS:1(official name : starved L1 ) 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. 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_LSY-2_GFP_Starved_Input_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1183692 Larvae_L1 NA GSE48716 LSY-2_GFP_L1_ChIP_Rep2 fed L1 OP367(official name : OP367 genotype : unc-119(ed3); wgIs367(lsy-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 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 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 : Bob Waterston's lab from UW ) Snyder_LSY-2_GFP_L1_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 WS180 Snyder_LSY-2_GFP_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183692_Snyder_LSY-2_GFP_L1_rep2-1.bedgraph.gz GSM1183690 Larvae_L1 NA GSE48716 LSY-2_GFP_L1_ChIP_Rep1 fed L1 OP367(official name : OP367 genotype : unc-119(ed3); wgIs367(lsy-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 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 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 : Bob Waterston's lab from UW ) Snyder_LSY-2_GFP_L1_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. 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_LSY-2_GFP_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183690_Snyder_LSY-2_GFP_L1_rep1-1.bedgraph.gz GSM1183648 Larvae_L1 NA GSE48706 pGES_HPL-2_lin-35_YL474_L1_ChIP_Rep2 starved L1 YL474(official name : YL474 genotype : lin-35(n745) I; unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and expressed in the intestine. The original transgene was subsequently crossed into a lin-35 mutant. made_by : Michelle Kudron in Reinke lab ) Snyder_pGHPL-2_lin-35_YL474_L1_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 WS180 Snyder_pGES_HPL-2_lin-35_YL474_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183648_Snyder_pGES_HPL-2_lin-35_YL474_L1_rep2-1.bedgraph.gz GSM1183646 Larvae_L1 NA GSE48706 pGES_HPL-2_lin-35_YL474_L1_ChIP_Rep1 starved L1 YL474(official name : YL474 genotype : lin-35(n745) I; unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and expressed in the intestine. The original transgene was subsequently crossed into a lin-35 mutant. made_by : Michelle Kudron in Reinke lab ) Snyder_pGHPL-2_lin-35_YL474_L1_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. 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_pGES_HPL-2_lin-35_YL474_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183646_Snyder_pGES_HPL-2_lin-35_YL474_L1_rep1-1.bedgraph.gz GSM1183636 Larvae_L1 NA GSE48703 N2_EFL-1_Ab_ChIP_Rep2 L1 larva DevStageWorm:L1 26dC:MS:1(official name : L1 26dC ) Snyder_N2_EFL-1_Ab_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_N2_EFL-1_Ab_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183636_Snyder_N2_EFL-1_Ab_rep2-1.bedgraph.gz GSM1183635 Larvae_L1 NA GSE48703 N2_EFL-1_Ab_Input_Rep2 L1 larva DevStageWorm:L1 26dC:MS:1(official name : L1 26dC ) 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_N2_EFL-1_Ab_Input_Rep2 bd_0_1_2_4_ce6 UsingSRR GSM1183634 Larvae_L1 NA GSE48703 N2_EFL-1_Ab_ChIP_Rep1 L1 larva DevStageWorm:L1 26dC:MS:1(official name : L1 26dC ) Snyder_N2_EFL-1_Ab_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_N2_EFL-1_Ab_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183634_Snyder_N2_EFL-1_Ab_rep1-1.bedgraph.gz GSM1183633 Larvae_L1 NA GSE48703 N2_EFL-1_Ab_Input_Rep1 L1 larva DevStageWorm:L1 26dC:MS:1(official name : L1 26dC ) 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_N2_EFL-1_Ab_Input_Rep1 bd_0_1_2_4_ce6 UsingSRR GSM1183632 Larvae_L1 NA GSE48702 GEI-11_GFP_L1_ChIP_Rep2 fed L1 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_L1_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_GEI-11_GFP_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183632_Snyder_GEI-11_GFP_L1_rep2-1.bedgraph.gz GSM1183630 Larvae_L1 NA GSE48702 GEI-11_GFP_L1_ChIP_Rep1 fed L1 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_L1_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_GEI-11_GFP_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183630_Snyder_GEI-11_GFP_L1_rep1-1.bedgraph.gz GSM1183612 Larvae_L1 NA GSE48697 LIN-35_GFP_L1_ChIP_Rep2 fed L1 YL409(official name : YL409 genotype : unc-119(ed3) III; vrIs60 [pLIN-35::LIN-35:GFP:FLAG::DPL-1 3'-UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by its own lin-35 promoter. made_by : Michelle Kudron (Valerie Reinke's lab) ) Snyder_LIN-35_GFP_L1_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 WS180 Snyder_LIN-35_GFP_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183612_Snyder_LIN-35_GFP_L1_rep2.bedgraph.gz GSM1183610 Larvae_L1 NA GSE48697 LIN-35_GFP_L1_ChIP_Rep1 fed L1 YL409(official name : YL409 genotype : unc-119(ed3) III; vrIs60 [pLIN-35::LIN-35:GFP:FLAG::DPL-1 3'-UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by its own lin-35 promoter. made_by : Michelle Kudron (Valerie Reinke's lab) ) Snyder_LIN-35_GFP_L1_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 WS180 Snyder_LIN-35_GFP_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183610_Snyder_LIN-35_GFP_L1_rep1-1.bedgraph.gz GSM1183608 Larvae_L1 NA GSE48696 DPL-1_GFP_L1_ChIP_Rep2 fed L1 YL448(official name : YL448 genotype : unc-119(ed3) III; vrIs83 [pGES-1::DPL-1::GFP FLAG: DPL-1 3'UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag made_by : Michelle Kudron (Valerie Reinke's lab) ) Snyder_DPL-1_GFP_L1_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_DPL-1_GFP_L1_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183608_Snyder_DPL-1_GFP_L1_rep2-1.bedgraph.gz GSM1183606 Larvae_L1 NA GSE48696 DPL-1_GFP_L1_ChIP_Rep1 fed L1 YL448(official name : YL448 genotype : unc-119(ed3) III; vrIs83 [pGES-1::DPL-1::GFP FLAG: DPL-1 3'UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag made_by : Michelle Kudron (Valerie Reinke's lab) ) Snyder_DPL-1_GFP_L1_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_DPL-1_GFP_L1_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183606_Snyder_DPL-1_GFP_L1_rep1-1.bedgraph.gz GSM1056282 Larvae_L1 NA GSE43087 Wild-Type (N2)Wild-type starved L1s L1 GRO-seq WS230 Libraries were sequenced with Illumina¡¯s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further. GRO-seq_N2_StarvedL1 other GSM1056282.bigwig GSM1138427 Larvae_L1 NA GSE46785 ZTF-4 L1 ChIPRep2 L1 26dC 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 L1 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 L1 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138427_Snyder_ZTF-4_GFP_L1_GFP_rep_2_120302_COLUMBO_00153_FC63BFU_L4_TGCT.bedgraph.gz GSM1138426 Larvae_L1 NA GSE46785 ZTF-4 L1 ChIPRep1 L1 26dC 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 L1 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 L1 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138426_Snyder_ZTF-4_GFP_L1_GFP_rep_1_120302_COLUMBO_00153_FC63BFU_L4_ACGT.bedgraph.gz GSM1138407 Larvae_L1 NA GSE46780 LIN-13 L1 ChIPRep2 L1 26dC 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 L1 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 L1 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138407_Snyder_LIN-13_GFP_L1_GFP_rep_2_120223_SPADE_00141_FC63BFT_L6_CATT.bedgraph.gz GSM1138406 Larvae_L1 NA GSE46780 LIN-13 L1 ChIPRep1 L1 26dC 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 L1 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 L1 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138406_Snyder_LIN-13_GFP_L1_GFP_rep_1_120223_SPADE_00141_FC63BFT_L6_GTAT.bedgraph.gz GSM1138367 Larvae_L1 NA GSE46770 JUN-1 L1 ChIPRep2 L1 26dC OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown ) JUN-1 GFP L1 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 JUN-1 GFP L1 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138367_Snyder_JUN-1_GFP_L1_GFP_rep_2_111215_SPADE_00129_FC64EJL_L6_CATT.bedgraph.gz GSM1138366 Larvae_L1 NA GSE46770 JUN-1 L1 ChIPRep1 L1 26dC OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown ) JUN-1 GFP L1 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 JUN-1 GFP L1 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138366_Snyder_JUN-1_GFP_L1_GFP_rep_1_111215_SPADE_00129_FC64EJL_L6_GTAT.bedgraph.gz GSM1076672 Larvae_L1 NA GSE44009 Snyder_ZK377.2_GFP_L1_rep2_GFP_CATT fed L1 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_L1_GFP_CATT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. 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_L1_rep2_GFP_CATT bg_0_1_2_4_ce10 GSM1076672_Snyder_ZK377.2_GFP_L1_rep2-1.bedgraph.gz GSM1076671 Larvae_L1 NA GSE44009 Snyder_ZK377.2_GFP_L1_rep1_GFP_GTAT fed L1 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_L1_GFP_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_ZK377.2_GFP_L1_rep1_GFP_GTAT bg_0_1_2_4_ce10 GSM1076671_Snyder_ZK377.2_GFP_L1_rep1-1.bedgraph.gz GSM1076668 Larvae_L1 NA GSE44008 Snyder_LIN-15B_GFP_L1_rep2_GFP_CATT fed L1 OP184(official name : OP184 genotype : unc119(ed3);wgIs184(lin-15B::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-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. made_by : S Kim ) Snyder_LIN-15B_GFP_L1_GFP_CATT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. 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_LIN-15B_GFP_L1_rep2_GFP_CATT bg_0_1_2_4_ce10 GSM1076668_Snyder_LIN-15B_GFP_L1_rep2.bedgraph.gz GSM1076667 Larvae_L1 NA GSE44008 Snyder_LIN-15B_GFP_L1_rep1_GFP_GTAT fed L1 OP184(official name : OP184 genotype : unc119(ed3);wgIs184(lin-15B::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-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. made_by : S Kim ) Snyder_LIN-15B_GFP_L1_GFP_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. 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_LIN-15B_GFP_L1_rep1_GFP_GTAT bg_0_1_2_4_ce10 GSM1076667_Snyder_LIN-15B_GFP_L1_rep1.bedgraph.gz GSM1076652 Larvae_L1 NA GSE44004 Snyder_C16A3.4_GFP_L1_rep2_CATT fed L1 OP345(official name : OP345 genotype : unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The C16A3.4::EGFP fusion protein has broad expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the C16A3.4 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_C16A3.4_GFP_L1_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_C16A3.4_GFP_L1_rep2_CATT bg_0_1_2_4_ce10 GSM1076652_Snyder_C16A3.4_GFP_L1_rep2.bedgraph.gz GSM1076651 Larvae_L1 NA GSE44004 Snyder_C16A3.4_GFP_L1_rep1_GTAT fed L1 OP345(official name : OP345 genotype : unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The C16A3.4::EGFP fusion protein has broad expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the C16A3.4 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_C16A3.4_GFP_L1_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_C16A3.4_GFP_L1_rep1_GTAT bg_0_1_2_4_ce10 GSM1076651_Snyder_C16A3.4_GFP_L1_rep1.bedgraph.gz GSM1076708 Larvae_L1 NA GSE44018 Snyder_DPL-1_GFP_L1v2_rep2_GFP_CATT fed L1 OP105(official name : OP105 genotype : unc119(ed3);wgIs105(dpl-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. The DPL-1::EGFP fusion protein has broad expression pattern description : but silence in germline cells. 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_DPL-1_GFP_L1v2_GTP_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. 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. 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_DPL-1_GFP_L1v2_rep2_GTP_CATT bg_0_1_2_4_ce10 GSM1076708_Snyder_DPL-1_GFP_L1v2_rep2.bedgraph.gz GSM1076707 Larvae_L1 NA GSE44018 Snyder_DPL-1_GFP_L1v2_rep1_GFP_GTAT fed L1 OP105(official name : OP105 genotype : unc119(ed3);wgIs105(dpl-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. The DPL-1::EGFP fusion protein has broad expression pattern description : but silence in germline cells. 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_DPL-1_GFP_L1v2_GFP_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_DPL-1_GFP_L1v2_rep1_GFP_GTAT bg_0_1_2_4_ce10 GSM1076707_Snyder_DPL-1_GFP_L1v2_rep1.bedgraph.gz GSM1076704 Larvae_L1 NA GSE44017 Snyder_Pges-1_HPL-2_YL416_L1_rep2_GFP_ACGT fed L1 YL416(official name : YL416 genotype : unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ) Snyder_Pges-1_HPL-2_YL416_L1_GFP_ACGT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_Pges-1_HPL-2_YL416_L1_rep2_GFP_ACGT bg_0_1_2_4_ce10 GSM1076704_Snyder_Pges-1_HPL-2_YL416_L1_rep2-1.bedgraph.gz GSM1076703 Larvae_L1 NA GSE44017 Snyder_Pges-1_HPL-2_YL416_L1_rep1_GFP_ACGT fed L1 YL416(official name : YL416 genotype : unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ) Snyder_Pges-1_HPL-2_YL416_L1_GFP_ACGT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. 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_Pges-1_HPL-2_YL416_L1_rep1_GFP_ACGT bg_0_1_2_4_ce10 GSM1076703_Snyder_Pges-1_HPL-2_YL416_L1_rep1-1.bedgraph.gz GSM1076700 Larvae_L1 NA GSE44016 Snyder_Pges-1_LIN-35_YL398_L1_rep2_GFP_GTAT fed L1 YL398(official name : YL398 genotype : unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ) Snyder_Pges-1_LIN-35_YL398_L1_GFP_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. 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_Pges-1_LIN-35_YL398_L1_rep2_GFP_GTAT bg_0_1_2_4_ce10 GSM1076700_Snyder_Pges-1_LIN-35_YL398_L1_rep2-1.bedgraph.gz GSM1076699 Larvae_L1 NA GSE44016 Snyder_Pges-1_LIN-35_YL398_L1_rep1_GFP_GTAT fed L1 YL398(official name : YL398 genotype : unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ) Snyder_Pges-1_LIN-35_YL398_L1_GFP_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. 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_Pges-1_LIN-35_YL398_L1_rep1_GFP_GTAT bg_0_1_2_4_ce10 GSM1076699_Snyder_Pges-1_LIN-35_YL398_L1_rep1.bedgraph.gz GSM1076692 Larvae_L1 NA GSE44014 Snyder_SPTF-1_GFP_L1_rep2_GFP_CATT fed L1 OP196(official name : OP196 genotype : unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119) outcross : 3 transgene : sptf-1 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 SPTF-1::EGFP fusion protein is expressed in the correct sptf-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SPTF-1 transcription factor. made_by : S Kim ) Snyder_SPTF-1_GFP_L1_GFP_CATT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. 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_SPTF-1_GFP_L1_rep2_GFP_CATT bg_0_1_2_4_ce10 GSM1076692_Snyder_SPTF-1_GFP_L1_rep2.bedgraph.gz GSM1076691 Larvae_L1 NA GSE44014 Snyder_SPTF-1_GFP_L1_rep1_GFP_GTAT fed L1 OP196(official name : OP196 genotype : unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119) outcross : 3 transgene : sptf-1 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 SPTF-1::EGFP fusion protein is expressed in the correct sptf-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SPTF-1 transcription factor. made_by : S Kim ) Snyder_SPTF-1_GFP_L1_GFP_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. 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_SPTF-1_GFP_L1_rep1_GFP_GTAT bg_0_1_2_4_ce10 GSM1076691_Snyder_SPTF-1_GFP_L1_rep1.bedgraph.gz GSM1076684 Larvae_L1 NA GSE44012 Snyder_NHR-77_GFP_L1_rep2_GFP_TGCT fed L1 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_L1_GFP_TGCT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. 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_L1_rep2_GFP_TGCT bg_0_1_2_4_ce10 GSM1076684_Snyder_NHR-77_GFP_L1_rep2-1.bedgraph.gz GSM1076683 Larvae_L1 NA GSE44012 Snyder_NHR-77_GFP_L1_rep1_GFP_ACGT fed L1 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_L1_GFP_ACGT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. 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_L1_rep1_GFP_ACGT bg_0_1_2_4_ce10 GSM1076683_Snyder_NHR-77_GFP_L1_rep1.bedgraph.gz GSM929333 Larvae_L1 NA GSE37884 Snyder_F45C12.2_GFP_L1_rep2 fed L1 OP212(official name : OP212 genotype : unc-119(ed3); wgIs212(F45C12.2: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 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_L1 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_F45C12.2_GFP_L1_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929332 Larvae_L1 NA GSE37884 Snyder_F45C12.2_GFP_L1_rep1 fed L1 OP212(official name : OP212 genotype : unc-119(ed3); wgIs212(F45C12.2: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 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_L1 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_F45C12.2_GFP_L1_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929301 Larvae_L1 NA GSE37876 Snyder_MEF-2_GFP_L1_rep2 fed L1 OP301(official name : OP301 genotype : unc119(ed3);wgIs301(mef-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 MEF-2::EGFP fusion protein is expressed in the correct mef-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MEF-2 transcription factor. made_by : R Waterston ) Snyder_MEF-2_GFP_L1 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_MEF-2_GFP_L1_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929300 Larvae_L1 NA GSE37876 Snyder_MEF-2_GFP_L1_rep1 fed L1 OP301(official name : OP301 genotype : unc119(ed3);wgIs301(mef-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 MEF-2::EGFP fusion protein is expressed in the correct mef-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MEF-2 transcription factor. made_by : R Waterston ) Snyder_MEF-2_GFP_L1 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_MEF-2_GFP_L1_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928363 Larvae_L1 NA GSE37808 Snyder_F16B12.6_GFP_L1_rep2 fed L1 OP114(official name : OP114 genotype : unc119(ed3);wgIs114(F16B12.6::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 F16B12.6::EGFP fusion protein is expressed in the correct F16B12.6 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F16B12.6 transcription factor. made_by : R Waterston ) Snyder_F16B12.6_GFP_L1 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_F16B12.6_GFP_L1_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928362 Larvae_L1 NA GSE37808 Snyder_F16B12.6_GFP_L1_rep1 fed L1 OP114(official name : OP114 genotype : unc119(ed3);wgIs114(F16B12.6::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 F16B12.6::EGFP fusion protein is expressed in the correct F16B12.6 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F16B12.6 transcription factor. made_by : R Waterston ) Snyder_F16B12.6_GFP_L1 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_F16B12.6_GFP_L1_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928343 Larvae_L1 NA GSE37803 Snyder_CES1_GFP_L1_rep2 fed L1 OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim ) Snyder_CES1_GFP_L1 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_CES1_GFP_L1_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928342 Larvae_L1 NA GSE37803 Snyder_CES1_GFP_L1_rep1 fed L1 OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim ) Snyder_CES1_GFP_L1 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_CES1_GFP_L1_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928339 Larvae_L1 NA GSE37802 Snyder_Pdpl1_DPL1_GFP_L1_rep2 fed L1 YL425(official name : YL425 genotype : unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ) Snyder_Pdpl1_DPL1_GFP_L1 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_Pdpl1_DPL1_GFP_L1_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928338 Larvae_L1 NA GSE37802 Snyder_Pdpl1_DPL1_GFP_L1_rep1 fed L1 YL425(official name : YL425 genotype : unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ) Snyder_Pdpl1_DPL1_GFP_L1 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_Pdpl1_DPL1_GFP_L1_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928335 Larvae_L1 NA GSE37801 Snyder_Pefl1_EFL1_GFP_L1_rep2 fed L1 YL424(official name : YL424 genotype : unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ) Snyder_Pefl1_EFL1_GFP_L1 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_Pefl1_EFL1_GFP_L1_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928334 Larvae_L1 NA GSE37801 Snyder_Pefl1_EFL1_GFP_L1_rep1 fed L1 YL424(official name : YL424 genotype : unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ) Snyder_Pefl1_EFL1_GFP_L1 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_Pefl1_EFL1_GFP_L1_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM876928 Larvae_L1 NA GSE35868 Snyder_FOS-1_GFP_L1_rep1 extraction1_seq1 fed L1 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_L1 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_FOS-1_GFP_L1_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM876929 Larvae_L1 NA GSE35868 Snyder_FOS-1_GFP_L1_rep2 extraction1_seq1 fed L1 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_L1 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_FOS-1_GFP_L1_rep2 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729383 Larvae_L1 NA GSE29482 Snyder_ALY-2_GFP_L1_rep2 extraction4_seq4 channel_1 fed L1 OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ) Snyder_ALY-2_GFP_L1 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_ALY-2_GFP_L1_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729382 Larvae_L1 NA GSE29482 Snyder_ALY-2_GFP_L1_rep1 extraction3_seq3 channel_1 fed L1 OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ) Snyder_ALY-2_GFP_L1 extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_ALY-2_GFP_L1_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729363 Larvae_L1 NA GSE29477 Snyder_ZAG-1_GFP_L1_rep2 extraction4_seq4 channel_1 fed L1 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_L1 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_L1_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729362 Larvae_L1 NA GSE29477 Snyder_ZAG-1_GFP_L1_rep1 extraction3_seq3 channel_1 fed L1 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_L1 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_ZAG-1_GFP_L1_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729355 Larvae_L1 NA GSE29475 Snyder_UNC-62_GFP_L1_rep2 extraction4_seq4 channel_1 fed L1 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_L1 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_L1_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729354 Larvae_L1 NA GSE29475 Snyder_UNC-62_GFP_L1_rep1 extraction3_seq3 channel_1 fed L1 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_L1 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_L1_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729303 Larvae_L1 NA GSE29462 Snyder_TLP-1_GFP_L1_rep2 extraction4_seq4 channel_1 fed L1 OP321(official name : TLP-1 genotype : unc119(ed3);wgIs321(tlp-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 biolistic transformation of an unc-119(ed3) strain. The spatio-temporal expression pattern of TLP-1::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 TLP-1 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_TLP-1_GFP_L1 extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_TLP-1_GFP_L1_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729302 Larvae_L1 NA GSE29462 Snyder_TLP-1_GFP_L1_rep1 extraction3_seq3 channel_1 fed L1 OP321(official name : TLP-1 genotype : unc119(ed3);wgIs321(tlp-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 biolistic transformation of an unc-119(ed3) strain. The spatio-temporal expression pattern of TLP-1::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 TLP-1 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_TLP-1_GFP_L1 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_TLP-1_GFP_L1_rep1 extraction3_seq3 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM677634 Larvae_L1 NA GSE25790 Snyder_N2_POLII_L1_rep2 extraction2_seq1 channel_2 fed L1 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_L1_rep2 extraction2_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR GSM677632 Larvae_L1 NA GSE25790 Snyder_N2_POLII_L1_rep1 extraction1_seq1 channel_2 fed L1 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_L1_rep1 extraction1_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR GSM391299 Larvae_L1 GSM363863 GSE15628 pha-4 transgenic worm OP37 starved L1 OP37 POLR2A ChIP-Seq Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp. Pha-4 starved L1 replicate 2 POL II bd_0_1_2_6_ce10 UsingSRR GSM391298 Larvae_L1 GSM363863 GSE15628 pha-4 transgenic worm OP37 starved L1 OP37 POLR2A ChIP-Seq Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp. Pha-4 starved L1 replicate 1 POL II bd_0_1_2_6_ce10 UsingSRR GSM351159 Larvae_L1 GSM351163 GSE14009 1hr recovery from 12hr L1 arrest POLR2A ChIP-Seq Data were analyzed using the Python package ERANGE. 6hr_Starved_S2 and 6hr_Starved_S2#2 were pooled prior to analysis and analyzed under the name 6hr_Starved_S2. The number of reads was counted over each gene model and over a 200 bp window spanning the most 5¡¯ transcription start site for the input and each of the samples. Read density was computed from these counts by normalizing to reads per million per kilobase of sequence. The variance in input read density correlates with the variance in sample read density even after subtracting input read density from sample density, as if sequence-specific biases have a multiplicative effect during library preparation and sequencing. GC content is one possible explanation for this phenomenon. We therefore chose to divide sample read density for each region by input read density, rather than using subtraction, resulting in data with fold-enrichment (relative to input) as the unit. To avoid undefined and volatile ratios, we actually used the larger of the input read density or the median of all input read densities, making a conservative adjustment to fold-enrichment assessments. 5¡¯ bias was defined as the ratio of fold-enrichment in the 200 bp window spanning the transcription start site to fold-enrichment over the gene model. To avoid undefined ratios in computing 5¡¯ bias, fold-enrichments in the denominator (gene model) of zero were changed to 0.1. 1hr_Recovery_8WG16 bd_0_1_2_6_ce10 UsingSRR GSM351155 Larvae_L1 GSM351162 GSE14009 12hr L1 arrest POLR2A ChIP-Seq Data were analyzed using the Python package ERANGE. 6hr_Starved_S2 and 6hr_Starved_S2#2 were pooled prior to analysis and analyzed under the name 6hr_Starved_S2. The number of reads was counted over each gene model and over a 200 bp window spanning the most 5¡¯ transcription start site for the input and each of the samples. Read density was computed from these counts by normalizing to reads per million per kilobase of sequence. The variance in input read density correlates with the variance in sample read density even after subtracting input read density from sample density, as if sequence-specific biases have a multiplicative effect during library preparation and sequencing. GC content is one possible explanation for this phenomenon. We therefore chose to divide sample read density for each region by input read density, rather than using subtraction, resulting in data with fold-enrichment (relative to input) as the unit. To avoid undefined and volatile ratios, we actually used the larger of the input read density or the median of all input read densities, making a conservative adjustment to fold-enrichment assessments. 5¡¯ bias was defined as the ratio of fold-enrichment in the 200 bp window spanning the transcription start site to fold-enrichment over the gene model. To avoid undefined ratios in computing 5¡¯ bias, fold-enrichments in the denominator (gene model) of zero were changed to 0.1. 12hr_Starved_8WG16 bd_0_1_2_6_ce10 UsingSRR