GSM3019581 Larvae_L4 NA GSE110969 whole worm L4 N2 MRG-1 ChIP-Seq ce10 Basecalling and Demultiplexing was done with Illumina bcl2fastq v2.18.0.12 software. N2 rep3 bd_0_1_2_7_ce10 GSM3019581_Peaks_N2_mrg1.AB3_peaks.narrowPeak.gz GSM3019580 Larvae_L4 NA GSE110969 whole worm L4 N2 MRG-1 ChIP-Seq ce10 Basecalling and Demultiplexing was done with Illumina bcl2fastq v2.18.0.12 software. N2 rep2 bd_0_1_2_7_ce10 GSM3019580_Peaks_N2_mrg1.AB2_peaks.narrowPeak.gz GSM3019579 Larvae_L4 NA GSE110969 whole worm L4 N2 MRG-1 ChIP-Seq ce10 Basecalling and Demultiplexing was done with Illumina bcl2fastq v2.18.0.12 software. N2 rep1 bd_0_1_2_7_ce10 GSM3019579_Peaks_N2_mrg1.AB1_peaks.narrowPeak.gz GSM3019575 Larvae_L4 NA GSE110969 whole worm L4 SS104 glp-4(bn2) I. MRG-1 ChIP-Seq ce10 Basecalling and Demultiplexing was done with Illumina bcl2fastq v2.18.0.12 software. glp-4 rep3 bd_0_1_2_7_ce10 GSM3019575_Peaks_glp4_mrg1.AB3_peaks.narrowPeak.gz GSM3019574 Larvae_L4 NA GSE110969 whole worm L4 SS104 glp-4(bn2) I. MRG-1 ChIP-Seq ce10 Basecalling and Demultiplexing was done with Illumina bcl2fastq v2.18.0.12 software. glp-4 rep2 bd_0_1_2_7_ce10 GSM3019574_Peaks_glp4_mrg1.AB2_peaks.narrowPeak.gz GSM3019573 Larvae_L4 NA GSE110969 whole worm L4 SS104 glp-4(bn2) I. MRG-1 ChIP-Seq ce10 Basecalling and Demultiplexing was done with Illumina bcl2fastq v2.18.0.12 software. glp-4 rep1 bd_0_1_2_7_ce10 GSM3019573_Peaks_glp4_mrg1.AB1_peaks.narrowPeak.gz GSM3398126 Larvae_L4 NA GSE117724 Whole animal VL648_R24, whole animal L4 VL648 GFP ChIP-Seq ce10 ?The raw sequencing data were first clipped for adaptor sequences and then mapped to the C. elegans genome (ce10, UC Santa Cruz) by the Burrows-Wheeler Aligner algorithm (BWA MEM, BWA version 0.7.15). The output SAM files were processed and sorted with the Picard tools. The output mapping files (BAM files) were filtered with SAMtools to remove any read that had a mapping quality less than 10 (SAMtools view 每b 每q 10 input.bam > output.bam). Peaks were determined using MACS version 2.1 with the no-model parameter. The final set of peaks were called if the difference in intensity values of samples had a significance level of p-value < 0.01. VL648_R24 bd_0_1_2_6_ce10 UsingSRR GSM3398125 Larvae_L4 NA GSE117724 Whole animal VL648_DMSO, whole animal L4 VL648 GFP ChIP-Seq ce10 ?The raw sequencing data were first clipped for adaptor sequences and then mapped to the C. elegans genome (ce10, UC Santa Cruz) by the Burrows-Wheeler Aligner algorithm (BWA MEM, BWA version 0.7.15). The output SAM files were processed and sorted with the Picard tools. The output mapping files (BAM files) were filtered with SAMtools to remove any read that had a mapping quality less than 10 (SAMtools view 每b 每q 10 input.bam > output.bam). Peaks were determined using MACS version 2.1 with the no-model parameter. The final set of peaks were called if the difference in intensity values of samples had a significance level of p-value < 0.01. VL648_DMSO bd_0_1_2_6_ce10 UsingSRR GSM3127931 Larvae_L4 NA GSE98758 whole worms whole worms L4 hmg3haChIP2 ChIP-Seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as will as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. hmg3haChIP2: Hmg3-HA ChIP-seq rep2 bd_0_1_2_6_ce10 UsingSRR GSM3127930 Larvae_L4 NA GSE98758 whole worms whole worms L4 hmg3haChIP1 ChIP-Seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as will as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. hmg3haChIP1: Hmg3-HA ChIP-seq rep1 bd_0_1_2_6_ce10 UsingSRR GSM2715425 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. hmg-4 rep3 bd_0_1_2_6_ce10 UsingSRR GSM2715424 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. hmg-4 rep2 bd_0_1_2_6_ce10 UsingSRR GSM2715423 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. hmg-4 rep1 bd_0_1_2_6_ce10 UsingSRR GSM2715422 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. spt-16 rep3 bd_0_1_2_6_ce10 UsingSRR GSM2715420 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. spt-16 rep1 bd_0_1_2_6_ce10 UsingSRR GSM2715419 Larvae_L4 NA GSE98758 whole body whole worms L4 N2 ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. hmg-3 rep3 bd_0_1_2_6_ce10 UsingSRR GSM2715418 Larvae_L4 NA GSE98758 whole body whole worms L4 N2 ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. hmg-3 rep2 bd_0_1_2_6_ce10 UsingSRR GSM2715421 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. spt-16 rep2 bd_0_1_2_6_ce10 UsingSRR GSM2715417 Larvae_L4 NA GSE98758 whole body whole worms L4 N2 ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. hmg-3 rep1 bd_0_1_2_6_ce10 UsingSRR GSM2715416 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. Rluc rep3 bd_0_1_2_6_ce10 UsingSRR GSM2715415 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. Rluc rep2 bd_0_1_2_6_ce10 UsingSRR GSM2715414 Larvae_L4 NA GSE98758 whole body whole worms L4 SS104 [glp-4 (bn2) I.] ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. Rluc rep1 bd_0_1_2_6_ce10 UsingSRR GSM2715412 Larvae_L4 NA GSE98758 whole body whole worms L4 N2 ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. rluc hmg3 rep2 bd_0_1_2_6_ce10 UsingSRR GSM2715413 Larvae_L4 NA GSE98758 whole body whole worms L4 N2 ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. rluc hmg3 rep3 bd_0_1_2_6_ce10 UsingSRR GSM2715411 Larvae_L4 NA GSE98758 whole body whole worms L4 N2 ATAC-seq ce10 ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5＊end coordinate of the 每 strand read was less than or equal to the 5＊end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5＊ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as well as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors. rluc hmg3 rep1 bd_0_1_2_6_ce10 UsingSRR GSM3141763 Larvae_L4 NA GSE114494 L4 larvae N2 H3K4me1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_l4_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141762 Larvae_L4 NA GSE114494 L4 larvae N2 H3K4me1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_l4_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3141729 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 ATAC-Seq ce10 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_L4_ATAC-seq_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141728 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 ATAC-Seq ce10 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_L4_ATAC-seq_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3142727 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_800U_ml bw_0_1_2_4_ce10 GSM3142727_dnase_wt_l4_rep2_800U_ml.bw GSM3142726 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_400U_ml bw_0_1_2_4_ce10 GSM3142726_dnase_wt_l4_rep2_400U_ml.bw GSM3142725 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_200U_ml bw_0_1_2_4_ce10 GSM3142725_dnase_wt_l4_rep2_200U_ml.bw GSM3142724 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_100U_ml bw_0_1_2_4_ce10 GSM3142724_dnase_wt_l4_rep2_100U_ml.bw GSM3142723 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_50U_ml bw_0_1_2_4_ce10 GSM3142723_dnase_wt_l4_rep2_50U_ml.bw GSM3142722 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_25U_ml bw_0_1_2_4_ce10 GSM3142722_dnase_wt_l4_rep2_25U_ml.bw GSM3142721 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_10U_ml bw_0_1_2_4_ce10 GSM3142721_dnase_wt_l4_rep2_10U_ml.bw GSM3142720 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_5U_ml bw_0_1_2_4_ce10 GSM3142720_dnase_wt_l4_rep2_5U_ml.bw GSM3142719 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep2_2.5U_ml bw_0_1_2_4_ce10 GSM3142719_dnase_wt_l4_rep2_2.5U_ml.bw GSM3142718 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_800U_ml bw_0_1_2_4_ce10 GSM3142718_dnase_wt_l4_rep1_800U_ml.bw GSM3142717 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_400U_ml bw_0_1_2_4_ce10 GSM3142717_dnase_wt_l4_rep1_400U_ml.bw GSM3142716 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_200U_ml bw_0_1_2_4_ce10 GSM3142716_dnase_wt_l4_rep1_200U_ml.bw GSM3142715 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_100U_ml bw_0_1_2_4_ce10 GSM3142715_dnase_wt_l4_rep1_100U_ml.bw GSM3142714 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_50U_ml bw_0_1_2_4_ce10 GSM3142714_dnase_wt_l4_rep1_50U_ml.bw GSM3142713 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_25U_ml bw_0_1_2_4_ce10 GSM3142713_dnase_wt_l4_rep1_25U_ml.bw GSM3142710 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_2.5U_ml bw_0_1_2_4_ce10 GSM3142710_dnase_wt_l4_rep1_2.5U_ml.bw GSM3142711 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_5U_ml bw_0_1_2_4_ce10 GSM3142711_dnase_wt_l4_rep1_5U_ml.bw GSM3142712 Larvae_L4 NA GSE114494 L4 larvae wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_L4_DNase-seq_rep1_10U_ml bw_0_1_2_4_ce10 GSM3142712_dnase_wt_l4_rep1_10U_ml.bw GSM2747080 Larvae_L4 NA GSE97775 Whole worms L4 gfp (HW1023) XRN2_ChIP ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. XRN2_ChIP_rep2 bw_0_1_2_4_ce10 GSM2747080_XRN2_ChIP_rep2.bw GSM2747079 Larvae_L4 NA GSE97775 Whole worms L4 gfp (HW1023) XRN2_ChIP ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. XRN2_ChIP_rep1 bw_0_1_2_4_ce10 GSM2747079_XRN2_ChIP_rep1.bw GSM2577237 Larvae_L4 NA GSE97775 whole body L4 N2 (wild-type) POLR2A ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. PolII_ChIP_xrn-2(RNAi)_IP_rep2 bw_0_1_2_4_ce10 GSM2577237_xrn2_RNAi_PolII_IP_2.bw GSM2577236 Larvae_L4 NA GSE97775 whole body L4 N2 (wild-type) POLR2A ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. PolII_ChIP_xrn-2(RNAi)_IP_rep1 bw_0_1_2_4_ce10 GSM2577236_xrn2_RNAI_PolII_IP_1.bw GSM2577234 Larvae_L4 NA GSE97775 whole body L4 N2 (wild-type) POLR2A ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. PolII_ChIP_mock(RNAi)_IP_rep1 bw_0_1_2_4_ce10 GSM2577234_mock_PolII_IP_1.bw GSM2577235 Larvae_L4 NA GSE97775 whole body L4 N2 (wild-type) POLR2A ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. PolII_ChIP_mock(RNAi)_IP_rep2 bw_0_1_2_4_ce10 GSM2577235_mock_PolII_IP_2.bw GSM2545812 Larvae_L4 NA GSE96908 whole animal whole animal L4 stage L4 sgIs2 (Strain I) L4 ChIP-seq ChIP-Seq ce6 ChIP sequence fragments were mapped to the C. elegans genome (version ce6) using the Short Read Mapping Package (SHRiMP) alignment tool using the R/Bioconductor package BSgenome.Celegans.UCSC.ce6 L4 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM1291066 Larvae_L4 NA GSE53412 whole animal staged L4 larvae from OP179 (SNPC-4-GFP transgenic strain) L4 OP179 GFP ChIP-Seq WS215 [ChIP-Seq] FASTQ files were processed and mapped using BWA (Li et al., 2009), retaining only high quality alignments (Q ≡ 30). SNPC-4 ChIP in staged L4s (5%) bg_0_1_2_4_ce10 GSM1291066_SNPC4_L4_IP_Rep0.density.scaled.bedgraph.gz GSM1183836 Larvae_L4 NA GSE48751 HLH-30_GFP_L4_ChIP_Rep2 L4 OP433(official name : OP433 genotype : unc-119(ed3) III; wgIs433(hlh-30::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HLH-30::EGFP fusion protein is expressed in the correct hlh-30 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-30 transcription factor. made_by : Unknown ) Snyder_HLH-30_GFP_L4_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_HLH-30_GFP_L4_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183836_Snyder_HLH-30_GFP_L4_GFP_rep_2_120228_MAGNUM_00133_FC63B9P_L4_TGCT.bedgraph.gz GSM1183834 Larvae_L4 NA GSE48751 HLH-30_GFP_L4_ChIP_Rep1 L4 OP433(official name : OP433 genotype : unc-119(ed3) III; wgIs433(hlh-30::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HLH-30::EGFP fusion protein is expressed in the correct hlh-30 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-30 transcription factor. made_by : Unknown ) Snyder_HLH-30_GFP_L4_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_HLH-30_GFP_L4_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183834_Snyder_HLH-30_GFP_L4_GFP_rep_1_120228_MAGNUM_00133_FC63B9P_L4_ACGT.bedgraph.gz GSM1183824 Larvae_L4 NA GSE48748 DVE-1_GFP_L4_ChIP_Rep2 L4 OP398(official name : OP398 genotype : unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by : Unknown ) Snyder_DVE-1_GFP_L4_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_DVE-1_GFP_L4_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183824_Snyder_DVE-1_GFP_L4_GFP_rep_2_120216_SPADE_00140_FC63BFJ_L7_GTAT.bedgraph.gz GSM1183822 Larvae_L4 NA GSE48748 DVE-1_GFP_L4_ChIP_Rep1 L4 OP398(official name : OP398 genotype : unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by : Unknown ) Snyder_DVE-1_GFP_L4_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_DVE-1_GFP_L4_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183822_Snyder_DVE-1_GFP_L4_GFP_rep_1_120214_SPADE_00139_FC63BFR_L8_TGCT.bedgraph.gz GSM1183820 Larvae_L4 NA GSE48747 ZIP-2_GFP_L4_ChIP_Rep2 L4 OP432(official name : OP432 genotype : unc-119(ed3) III; wgIs432(zip-2::TY1-GFP-3xFLA;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZIP-2::EGFP fusion protein is expressed in the correct zip-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZIP-2 transcription factor. made_by : Unknown ) Snyder_ZIP-2_GFP_L4_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_ZIP-2_GFP_L4_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183820_Snyder_ZIP-2_GFP_L4_GFP_rep_2_120316_ROCKFORD_00135_FC64KNR_L6_CATT.bedgraph.gz GSM1183818 Larvae_L4 NA GSE48747 ZIP-2_GFP_L4_ChIP_Rep1 L4 OP432(official name : OP432 genotype : unc-119(ed3) III; wgIs432(zip-2::TY1-GFP-3xFLA;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZIP-2::EGFP fusion protein is expressed in the correct zip-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZIP-2 transcription factor. made_by : Unknown ) Snyder_ZIP-2_GFP_L4_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_ZIP-2_GFP_L4_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183818_Snyder_ZIP-2_GFP_L4_GFP_rep_1_120316_ROCKFORD_00135_FC64KNR_L6_GTAT.bedgraph.gz GSM1183776 Larvae_L4 NA GSE48737 FKH-10_GFP_L4_ChIP_Rep2 L4 OP337(official name : OP337 genotype : unc119(ed3);wgIs377(fkh-10::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FKH-10::EGFP fusion protein is expressed in the correct fkh-10 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FKH-10 transcription factor. made_by : Unknown ) Snyder_FKH-10_GFP_L4_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_FKH-10_GFP_L4_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183776_Snyder_FKH-10_GFP_L4_GFP_rep_2_111007_SPADE_00112_FC64KFC_L4_TGCT.bedgraph.gz GSM1183774 Larvae_L4 NA GSE48737 FKH-10_GFP_L4_ChIP_Rep1 L4 OP337(official name : OP337 genotype : unc119(ed3);wgIs377(fkh-10::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FKH-10::EGFP fusion protein is expressed in the correct fkh-10 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FKH-10 transcription factor. made_by : Unknown ) Snyder_FKH-10_GFP_L4_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_FKH-10_GFP_L4_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183774_Snyder_FKH-10_GFP_L4_GFP_rep_1_111007_SPADE_00112_FC64KFC_L4_ACGT.bedgraph.gz GSM1183748 Larvae_L4 NA GSE48730 UNC_62_GFP_L4_ChIP_Rep2 L4 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_L4_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_UNC_62_GFP_L4_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183748_Snyder_UNC_62_GFP_L4_GFP_rep_2_110915_SPADE_00108_FC631JC_L7_CATT.bedgraph.gz GSM1183746 Larvae_L4 NA GSE48730 UNC_62_GFP_L4_ChIP_Rep1 L4 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_L4_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_UNC_62_GFP_L4_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183746_Snyder_UNC_62_GFP_L4_GFP_rep_1_110915_SPADE_00108_FC631JC_L7_GTAT.bedgraph.gz GSM1183744 Larvae_L4 NA GSE48729 LIN-39_GFP_L4_ChIP_Rep2 L4 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_L4_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_L4_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183744_Snyder_LIN-39_GFP_L4_GFP_rep_2_110915_SPADE_00108_FC631JC_L6_TGCT.bedgraph.gz GSM1183742 Larvae_L4 NA GSE48729 LIN-39_GFP_L4_ChIP_Rep1 L4 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_L4_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_L4_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183742_Snyder_LIN-39_GFP_L4_GFP_rep_1_110915_SPADE_00108_FC631JC_L6_ACGT.bedgraph.gz GSM1183736 Larvae_L4 NA GSE48727 NHR-11_GFP_L4_ChIP_Rep2 L4 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_L4_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_L4_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183736_Snyder_NHR-11_GFP_L4_GFP_rep_2_110912_COLUMBO_00109_FC631RL_L6_TGCT.bedgraph.gz GSM1183734 Larvae_L4 NA GSE48727 NHR-11_GFP_L4_ChIP_Rep1 L4 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_L4_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NHR-11_GFP_L4_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183734_Snyder_NHR-11_GFP_L4_GFP_rep_1_110912_COLUMBO_00109_FC631RL_L6_ACGT.bedgraph.gz GSM1138447 Larvae_L4 NA GSE46790 LSY-2 L4 v2 ChIPRep2 L4 OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ) LSY-2 GFP L4 v2 C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 LSY-2 GFP L4 v2 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138447_Snyder_LSY-2_GFP_L4_GFP_rep_2_120306_COLUMBO_00154_FC64V9L_L3_TGCT.bedgraph.gz GSM1138446 Larvae_L4 NA GSE46790 LSY-2 L4 v2 ChIPRep1 L4 OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ) LSY-2 GFP L4 v2 C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 LSY-2 GFP L4 v2 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138446_Snyder_LSY-2_GFP_L4_GFP_rep_1_120306_COLUMBO_00154_FC64V9L_L3_ACGT.bedgraph.gz GSM1138435 Larvae_L4 NA GSE46787 CEH-28 L4 ChIPRep2 L4 OP241(official name : OP241 genotype : unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by : Unknwon ) CEH-28 GFP L4 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 CEH-28 GFP L4 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138435_Snyder_CEH-28_GFP_L4_GFP_rep_2_120306_COLUMBO_00154_FC64V9L_L4_TGCT.bedgraph.gz GSM1138434 Larvae_L4 NA GSE46787 CEH-28 L4 ChIPRep1 L4 OP241(official name : OP241 genotype : unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by : Unknwon ) CEH-28 GFP L4 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 CEH-28 GFP L4 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138434_Snyder_CEH-28_GFP_L4_GFP_rep_1_120306_COLUMBO_00154_FC64V9L_L4_ACGT.bedgraph.gz GSM1138431 Larvae_L4 NA GSE46786 NHR-10 L4 ChIPRep2 L4 OP239(official name : OP239 genotype : unc119(ed3);wgIs239(nhr-10::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-10::EGFP fusion protein is expressed in the correct nhr-10 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-10 transcription factor. made_by : Unknown ) NHR-10 GFP L4 C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 NHR-10 GFP L4 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138431_Snyder_NHR-10_GFP_L4_GFP_rep_2_120305_MAGNUM_00135_FC63BA5_L4_CATT.bedgraph.gz GSM1138430 Larvae_L4 NA GSE46786 NHR-10 L4 ChIPRep1 L4 OP239(official name : OP239 genotype : unc119(ed3);wgIs239(nhr-10::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-10::EGFP fusion protein is expressed in the correct nhr-10 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-10 transcription factor. made_by : Unknown ) NHR-10 GFP L4 C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 NHR-10 GFP L4 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138430_Snyder_NHR-10_GFP_L4_GFP_rep_1_120305_MAGNUM_00135_FC63BA5_L4_GTAT.bedgraph.gz GSM1138415 Larvae_L4 NA GSE46782 LIN-13 L4 ChIPRep2 L4 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 L4 C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 LIN-13 GFP L4 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138415_Snyder_LIN-13_GFP_L4_GFP_rep_2_120224_MAGNUM_00132_FC63BBD_L3_CATT.bedgraph.gz GSM1138414 Larvae_L4 NA GSE46782 LIN-13 L4 ChIPRep1 L4 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 L4 C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 LIN-13 GFP L4 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138414_Snyder_LIN-13_GFP_L4_GFP_rep_1_120224_MAGNUM_00132_FC63BBD_L3_GTAT.bedgraph.gz GSM1138375 Larvae_L4 NA GSE46772 SKN-1 L4 ChIPRep2 L4 OP342(official name : OP342 genotype : unc119(ed3);wgIs341(skn-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ) SKN-1 GFP L4 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 SKN-1 GFP L4 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138375_Snyder_SKN-1_GFP_L4_GFP_rep_2_111110_KOJAK_00069_FC64FPY_L8_CATT.bedgraph.gz GSM1138374 Larvae_L4 NA GSE46772 SKN-1 L4 ChIPRep1 L4 OP342(official name : OP342 genotype : unc119(ed3);wgIs341(skn-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ) SKN-1 GFP L4 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 SKN-1 GFP L4 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138374_Snyder_SKN-1_GFP_L4_GFP_rep_1_111110_KOJAK_00069_FC64FPY_L8_GTAT.bedgraph.gz GSM1138363 Larvae_L4 NA GSE46769 NHR-76 L4 ChIPRep2 L4 OP203(official name : OP203 genotype : unc-119(ed3); wgIs203(nhr-76::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 NHR-76::EGFP fusion protein is expressed in the correct nhr-76 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-76 transcription factor. made_by : R. Waterston ) NHR-76 GFP L4 C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 NHR-76 GFP L4 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138363_Snyder_NHR-76_GFP_L4_GFP_rep_2_120105_COLUMBO_00136_FC64YG5_L7_TGCT.bedgraph.gz GSM1138362 Larvae_L4 NA GSE46769 NHR-76 L4 ChIPRep1 L4 OP203(official name : OP203 genotype : unc-119(ed3); wgIs203(nhr-76::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 NHR-76::EGFP fusion protein is expressed in the correct nhr-76 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-76 transcription factor. made_by : R. Waterston ) NHR-76 GFP L4 C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 NHR-76 GFP L4 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138362_Snyder_NHR-76_GFP_L4_GFP_rep_1_120105_COLUMBO_00136_FC64YG5_L7_ACGT.bedgraph.gz GSM1138359 Larvae_L4 NA GSE46768 ZTF-11 L4 ChIPRep2 L4 OP236(official name : OP236 genotype : unc119(ed3);wgIs236(elk-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown ) ZTF-11 GFP L4 C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 ZTF-11 GFP L4 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138359_Snyder_ZTF-11_GFP_L4_GFP_rep_2_120105_COLUMBO_00136_FC64YG5_L7_CATT.bedgraph.gz GSM1138358 Larvae_L4 NA GSE46768 ZTF-11 L4 ChIPRep1 L4 OP236(official name : OP236 genotype : unc119(ed3);wgIs236(elk-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown ) ZTF-11 GFP L4 C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 ZTF-11 GFP L4 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138358_Snyder_ZTF-11_GFP_L4_GFP_rep_1_120105_COLUMBO_00136_FC64YG5_L7_GTAT.bedgraph.gz GSM1138351 Larvae_L4 NA GSE46766 JUN-1 L4 ChIPRep2 L4 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 L4 C.elJUN-1 GFP L4 C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 JUN-1 GFP L4 C.elJUN-1 GFP L4 C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138351_Snyder_JUN-1_GFP_L4_GFP_rep_2_120105_COLUMBO_00136_FC64YG5_L6_CATT.bedgraph.gz GSM1138350 Larvae_L4 NA GSE46766 JUN-1 L4 ChIPRep1 L4 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 L4 C.elJUN-1 GFP L4 C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 JUN-1 GFP L4 C.elJUN-1 GFP L4 C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138350_Snyder_JUN-1_GFP_L4_GFP_rep_1_120105_COLUMBO_00136_FC64YG5_L6_GTAT.bedgraph.gz GSM1076680 Larvae_L4 NA GSE44011 Snyder_ZK377.2_GFP_L4_rep2_GFP_TGCT L4 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_L4_GFP_TGCT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_ZK377.2_GFP_L4_rep2_GFP_TGCT bg_0_1_2_4_ce10 GSM1076680_Snyder_ZK377.2_GFP_L4_rep2-1.bedgraph.gz GSM1076679 Larvae_L4 NA GSE44011 Snyder_ZK377.2_GFP_L4_rep1_GFP_ACGT L4 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_L4_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_ZK377.2_GFP_L4_rep1_GFP_ACGT bg_0_1_2_4_ce10 GSM1076679_Snyder_ZK377.2_GFP_L4_rep1-1.bedgraph.gz GSM1076648 Larvae_L4 NA GSE44003 Snyder_DPL-1_GFP_L4_rep2_ACGT L4 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_L4_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_DPL-1_GFP_L4_rep2_ACGT bg_0_1_2_4_ce10 GSM1076648_Snyder_DPL-1_GFP_L4_rep2-1.bedgraph.gz GSM1076647 Larvae_L4 NA GSE44003 Snyder_DPL-1_GFP_L4_rep1_TGCT L4 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_L4_TGCT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_DPL-1_GFP_L4_rep1_TGCT bg_0_1_2_4_ce10 GSM1076647_Snyder_DPL-1_GFP_L4_rep1-1.bedgraph.gz GSM1076688 Larvae_L4 NA GSE44013 Snyder_NHR-116_GFP_L4_rep2_GFP_TGCT L4 OP226(official name : OP226 genotype : unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-116 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by : M Sarov ) Snyder_NHR-116_GFP_L4_GFP_TGCT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NHR-116_GFP_L4_rep2_GFP_TGCT bg_0_1_2_4_ce10 GSM1076688_Snyder_NHR-116_GFP_L4_rep2-1.bedgraph.gz GSM1076687 Larvae_L4 NA GSE44013 Snyder_NHR-116_GFP_L4_rep1_GFP_ACGT L4 OP226(official name : OP226 genotype : unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-116 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by : M Sarov ) Snyder_NHR-116_GFP_L4_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-116_GFP_L4_rep1_GFP_ACGT bg_0_1_2_4_ce10 GSM1076687_Snyder_NHR-116_GFP_L4_rep1-1.bedgraph.gz GSM942052 Larvae_L4 NA GSE38437 Snyder_ZAG-1_GFP_L4_rep2 L4 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_L4 extraction2_seq1 aliquote 1,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_ZAG-1_GFP_L4_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM942051 Larvae_L4 NA GSE38437 Snyder_ZAG-1_GFP_L4_rep1 L4 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_L4 extraction1_seq1 aliquote 1,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_ZAG-1_GFP_L4_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929325 Larvae_L4 NA GSE37882 Snyder_NHR-77_GFP_L4_rep2 L4 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_L4 extraction2_seq1 aliquote 1,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NHR-77_GFP_L4_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929324 Larvae_L4 NA GSE37882 Snyder_NHR-77_GFP_L4_rep1 L4 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_L4 extraction1_seq1 aliquote 1,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NHR-77_GFP_L4_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM929309 Larvae_L4 NA GSE37878 Snyder_FOS-1_GFP_L4_rep2 L4 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_L4 extraction2_seq1,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_FOS-1_GFP_L4_rep2 extraction2_seq1 bd_0_1_2_6_ce10 UsingSRR GSM929308 Larvae_L4 NA GSE37878 Snyder_FOS-1_GFP_L4_rep1 L4 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_L4 extraction1_seq1,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_FOS-1_GFP_L4_rep1 extraction1_seq1 bd_0_1_2_6_ce10 UsingSRR GSM709343 Young_adult NA GSE23042 hypodermis synchronized L4 synchronized L4 PD3995 hypodermis 2nd run,genomic DNA from synchronized young adult worms expressing DAM driven by rol-6 promoter ChIP-Seq WS170 We generated a database of all potential DAM tags with the structure 5'-(N)16GATC-3' from C. elegans genome version WS170. There are 269,049 DAM (GATC) sites per haploid genome in C. elegans. Because DALEC captures two tags (in principle) per GATC site, there are a total of 538,098 potential tags (or half sites) per haploid genome. To reduce computation time during alignment of Solexa reads to the genome, each tag was represented by a 16 nucleotide sequence that did not include the 3' GATC. We excluded DAM tags that occurred more than once in the genome or that mapped to vector or ribosomal sequences. We also excluded tags belonging to two adjacent GATC sites that lie within 20 bp from each other. Under situations where two fully methylated adjacent GATC sites mapped within 20 bp of each other, one site will always be captured at the expense of the other, resulting in undercount of DAM accessibility at such regions. When the distances are slightly above 20 bp, it is conceivable that there may be inherent bias in Mme I sequence preference that leads to the preferential capture of one site over the other, again resulting in undercount. To avoid both situations from skewing our analysis, we excluded such "proximal tags" using the criteria described in Additional File 2, Figure S4). After filtering out proximal, repetitive, and vector/ribosome-derived sequences, we were left with 370,152 in silico tags (per haploid genome) that we could use to align Solexa reads to the genome. Described in Sha et al. (BMC Genomics 2010, 11:465) hypodermis 2nd run bd_0_1_2_6_ce10 UsingSRR GSM709342 Young_adult NA GSE23042 hypodermis synchronized L4 synchronized L4 PD3995 hypodermis 1st run,genomic DNA from synchronized young adult worms expressing DAM driven by rol-6 promoter ChIP-Seq WS170 We generated a database of all potential DAM tags with the structure 5'-(N)16GATC-3' from C. elegans genome version WS170. There are 269,049 DAM (GATC) sites per haploid genome in C. elegans. Because DALEC captures two tags (in principle) per GATC site, there are a total of 538,098 potential tags (or half sites) per haploid genome. To reduce computation time during alignment of Solexa reads to the genome, each tag was represented by a 16 nucleotide sequence that did not include the 3' GATC. We excluded DAM tags that occurred more than once in the genome or that mapped to vector or ribosomal sequences. We also excluded tags belonging to two adjacent GATC sites that lie within 20 bp from each other. Under situations where two fully methylated adjacent GATC sites mapped within 20 bp of each other, one site will always be captured at the expense of the other, resulting in undercount of DAM accessibility at such regions. When the distances are slightly above 20 bp, it is conceivable that there may be inherent bias in Mme I sequence preference that leads to the preferential capture of one site over the other, again resulting in undercount. To avoid both situations from skewing our analysis, we excluded such "proximal tags" using the criteria described in Additional File 2, Figure S4). After filtering out proximal, repetitive, and vector/ribosome-derived sequences, we were left with 370,152 in silico tags (per haploid genome) that we could use to align Solexa reads to the genome. Described in Sha et al. (BMC Genomics 2010, 11:465) hypodermis 1st run bd_0_1_2_6_ce10 UsingSRR GSM700176 Larvae_L4 NA GSE26152 Snyder_PES-1_GFP_L4_rep2 extraction9_seq9 channel_1 L4 OP87(official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::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 PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ) Snyder_PES-1_GFP_L4 extraction9_seq9 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS190 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS190 Snyder_PES-1_GFP_L4_rep2 extraction9_seq9 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700175 Larvae_L4 NA GSE26152 Snyder_PES-1_GFP_L4_rep2 extraction8_seq8 channel_1 L4 OP87(official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::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 PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ) Snyder_PES-1_GFP_L4 extraction8_seq8 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS190 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS190 Snyder_PES-1_GFP_L4_rep2 extraction8_seq8 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700174 Larvae_L4 NA GSE26152 Snyder_PES-1_GFP_L4_rep2 extraction7_seq7 channel_1 L4 OP87(official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::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 PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ) Snyder_PES-1_GFP_L4 extraction7_seq7 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS190 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS190 Snyder_PES-1_GFP_L4_rep2 extraction7_seq7 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700169 Larvae_L4 NA GSE26152 Snyder_PES-1_GFP_L4_rep1 extraction2_seq2 channel_1 L4 OP87(official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::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 PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ) Snyder_PES-1_GFP_L4 extraction2_seq2 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS190 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS190 Snyder_PES-1_GFP_L4_rep1 extraction2_seq2 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700168 Larvae_L4 NA GSE26152 Snyder_PES-1_GFP_L4_rep1 extraction1_seq1 channel_1 L4 OP87(official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::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 PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ) Snyder_PES-1_GFP_L4 extraction1_seq1 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS190 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS190 Snyder_PES-1_GFP_L4_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM677646 Larvae_L4 NA GSE25793 Snyder_N2_POLII_L4_rep2 extraction2_seq1 channel_2 L4 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_L4_rep2 extraction2_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR GSM677644 Larvae_L4 NA GSE25793 Snyder_N2_POLII_L4_rep1 extraction1_seq1 channel_2 L4 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_L4_rep1 extraction1_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR