GSM3080184 Young_adult NA GSE112682 whole animal extract Young adults Young adults TOFU-5 ChIP-seq ChIP-Seq ce10 read trimming TOFU-5 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3080183 Young_adult NA GSE112682 whole animal extract Young adults Young adults TOFU-4 ChIP-seq ChIP-Seq ce10 read trimming TOFU-4 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3080182 Young_adult NA GSE112682 whole animal extract Young adults Young adults SNPC-4 ChIP-seq ChIP-Seq ce10 read trimming SNPC-4 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3080181 Young_adult NA GSE112682 whole animal extract Young adults Young adults PRDE-1 ChIP-seq ChIP-Seq ce10 read trimming PRDE-1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3305741 Young_adult NA GSE117662 C. elegans young adults young adult POLR2A ChIP-Seq WS190 Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis. set-32(red11); met-2(n4256) set-25(n5021) hrde-1(tm1200) mutant ChIP-Seq bd_0_1_2_6_ce10 UsingSRR GSM3305740 Young_adult NA GSE117662 C. elegans young adults young adult POLR2A ChIP-Seq WS190 Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis. met-2(n4256) set-25(n5021) hrde-1(tm1200) mutant ChIP-Seq bd_0_1_2_6_ce10 UsingSRR GSM3305739 Young_adult NA GSE117662 C. elegans young adults young adult POLR2A ChIP-Seq WS190 Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis. set-32(red11); hrde-1(tm1200) mutant ChIP-Seq bd_0_1_2_6_ce10 UsingSRR GSM3305738 Young_adult NA GSE117662 C. elegans young adults young adult POLR2A ChIP-Seq WS190 Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis. set-32(red11); met-2(n4256) set-25(n5021) mutant ChIP-Seq bd_0_1_2_6_ce10 UsingSRR GSM3305737 Young_adult NA GSE117662 C. elegans young adults young adult POLR2A ChIP-Seq WS190 Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis. met-2(n4256) set-25(n5021) mutant ChIP-Seq bd_0_1_2_6_ce10 UsingSRR GSM3305736 Young_adult NA GSE117662 C. elegans young adults young adult POLR2A ChIP-Seq WS190 Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis. set-32(red11) mutant ChIP-Seq bd_0_1_2_6_ce10 UsingSRR GSM3305735 Young_adult NA GSE117662 C. elegans young adults young adult POLR2A ChIP-Seq WS190 Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis. hrde-1 (tm1200) mutant ChIP-Seq bd_0_1_2_6_ce10 UsingSRR GSM3305734 Young_adult NA GSE117662 C. elegans young adults young adult POLR2A ChIP-Seq WS190 Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis. N2 ChIP-Seq 1 bd_0_1_2_6_ce10 UsingSRR GSM3141765 Young_adult NA GSE114494 young adults N2 H3K4me1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_ya_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141764 Young_adult NA GSE114494 young adults N2 H3K4me1 ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_ya_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3141733 Young_adult NA GSE114494 day 1 / young adults glp-1(e2144) ATAC-Seq ce10 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. glp-1_YA_ATAC-seq_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141732 Young_adult NA GSE114494 day 1 / young adults glp-1(e2144) ATAC-Seq ce10 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. glp-1_YA_ATAC-seq_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3141731 Young_adult NA GSE114494 young adults wild-type N2 ATAC-Seq ce10 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_YA_ATAC-seq_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141730 Young_adult NA GSE114494 young adults wild-type N2 ATAC-Seq ce10 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_YA_ATAC-seq_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3142744 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_800U_ml bw_0_1_2_4_ce10 GSM3142744_dnase_wt_ya_rep2_800U_ml.bw GSM3142743 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_400U_ml bw_0_1_2_4_ce10 GSM3142743_dnase_wt_ya_rep2_400U_ml.bw GSM3142742 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_200U_ml bw_0_1_2_4_ce10 GSM3142742_dnase_wt_ya_rep2_200U_ml.bw GSM3142741 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_100U_ml bw_0_1_2_4_ce10 GSM3142741_dnase_wt_ya_rep2_100U_ml.bw GSM3142740 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_50U_ml bw_0_1_2_4_ce10 GSM3142740_dnase_wt_ya_rep2_50U_ml.bw GSM3142739 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_25U_ml bw_0_1_2_4_ce10 GSM3142739_dnase_wt_ya_rep2_25U_ml.bw GSM3142738 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_10U_ml bw_0_1_2_4_ce10 GSM3142738_dnase_wt_ya_rep2_10U_ml.bw GSM3142737 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_5U_ml bw_0_1_2_4_ce10 GSM3142737_dnase_wt_ya_rep2_5U_ml.bw GSM3142736 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep2_2.5U_ml bw_0_1_2_4_ce10 GSM3142736_dnase_wt_ya_rep2_2.5U_ml.bw GSM3142735 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep1_800U_ml bw_0_1_2_4_ce10 GSM3142735_dnase_wt_ya_rep1_800U_ml.bw GSM3142734 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep1_400U_ml bw_0_1_2_4_ce10 GSM3142734_dnase_wt_ya_rep1_400U_ml.bw GSM3142733 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep1_200U_ml bw_0_1_2_4_ce10 GSM3142733_dnase_wt_ya_rep1_200U_ml.bw GSM3142732 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep1_100U_ml bw_0_1_2_4_ce10 GSM3142732_dnase_wt_ya_rep1_100U_ml.bw GSM3142731 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep1_50U_ml bw_0_1_2_4_ce10 GSM3142731_dnase_wt_ya_rep1_50U_ml.bw GSM3142730 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep1_25U_ml bw_0_1_2_4_ce10 GSM3142730_dnase_wt_ya_rep1_25U_ml.bw GSM3142729 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep1_10U_ml bw_0_1_2_4_ce10 GSM3142729_dnase_wt_ya_rep1_10U_ml.bw GSM3142728 Young_adult NA GSE114494 young adults wild-type N2 DNase ce10 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_YA_DNase-seq_rep1_2.5U_ml bw_0_1_2_4_ce10 GSM3142728_dnase_wt_ya_rep1_2.5U_ml.bw GSM2694119 Young_adult NA GSE100829 whole worm young adult tdp-1(ok803) HPL-2, Research provided by the Palladino lab ChIP-Seq ws220 Basecalls performed using CASAVA software from Illumina Tdp_1_Hpl2-2_ChIP bw_0_1_2_4_ce10 GSM2694119_tdp1-2_Hpl2_ChIP.bw GSM2694117 Young_adult NA GSE100829 whole worm young adult N2 (Bristol) HPL-2, Research provided by the Palladino lab ChIP-Seq ws220 Basecalls performed using CASAVA software from Illumina N2_Hpl2-2_ChIP bw_0_1_2_4_ce10 GSM2694117_N22_Hpl2_ChIP.bw GSM2694118 Young_adult NA GSE100829 whole worm young adult tdp-1(ok803) HPL-2, Research provided by the Palladino lab ChIP-Seq ws220 Basecalls performed using CASAVA software from Illumina Tdp_1_Hpl2-1_ChIP bw_0_1_2_4_ce10 GSM2694118_tdp1-1_HPL2Chip_subtractedControl.bw GSM2694116 Young_adult NA GSE100829 whole worm young adult N2 (Bristol) HPL-2, Research provided by the Palladino lab ChIP-Seq ws220 Basecalls performed using CASAVA software from Illumina N2_Hpl2-1_ChIP bw_0_1_2_4_ce10 GSM2694116_N21_Hpl2_ChIP.bw GSM2862375 Young_adult NA GSE107190 whole animal staged young adult (YA) from OP383 (OEF-1:GFP transgenic strain) YA OP383 GFP ChIP-Seq WS220 FASTQ files were processed and mapped using BWA (Li et al., 2009), retaining only high quality alignments (Q ¡Ý 30). OEF-1 ChIP in staged YA rep 2 bw_0_1_2_4_ce10 GSM2862375.bigwig GSM2862374 Young_adult NA GSE107190 whole animal staged young adult (YA) from OP383 (OEF-1:GFP transgenic strain) YA OP383 GFP ChIP-Seq WS220 FASTQ files were processed and mapped using BWA (Li et al., 2009), retaining only high quality alignments (Q ¡Ý 30). OEF-1 ChIP in staged YA rep 1 bd_0_1_2_6_ce10 UsingSRR GSM2385317 Young_adult NA GSE89608 whole organisms young adult N2 ATAC-seq ce10 Sequencing adaptors were trimmed using a custom script that aligns the 5¡¯ ends of the forward read and reverse complement of the reverse read, and then removes any aligning sequence (minimum length 3). Young adult replicate C bd_0_1_2_6_ce10 UsingSRR GSM2385314 Young_adult NA GSE89608 whole organisms young adult N2 ATAC-seq ce10 Sequencing adaptors were trimmed using a custom script that aligns the 5¡¯ ends of the forward read and reverse complement of the reverse read, and then removes any aligning sequence (minimum length 3). Young adult replicate B bd_0_1_2_6_ce10 UsingSRR GSM2385311 Young_adult NA GSE89608 whole organisms young adult N2 ATAC-seq ce10 Sequencing adaptors were trimmed using a custom script that aligns the 5¡¯ ends of the forward read and reverse complement of the reverse read, and then removes any aligning sequence (minimum length 3). Young adult replicate A bd_0_1_2_6_ce10 UsingSRR GSM2333110 Young_adult NA GSE87524 whole body young adults, MET-2 ChIP N2 MET-2 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. MET-2_YA_rep2 bw_0_1_2_4_ce10 GSM2333110_MET2_YA_ChIPseq_BEADSmapq0_rep2.bw GSM2333109 Young_adult NA GSE87524 whole body young adults, MET-2 ChIP N2 MET-2 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. MET-2_YA_rep1 bw_0_1_2_4_ce10 GSM2333109_MET2_YA_ChIPseq_BEADSmapq0_rep1.bw GSM2333108 Young_adult NA GSE87524 whole body young adults, LIN-61 ChIP N2 LIN-61 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. LIN-61_YA_rep2 bw_0_1_2_4_ce10 GSM2333108_LIN61_YA_ChIPseq_BEADSmapq0_rep2.bw GSM2333107 Young_adult NA GSE87524 whole body young adults, LIN-61 ChIP N2 LIN-61 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. LIN-61_YA_rep1 bw_0_1_2_4_ce10 GSM2333107_LIN61_YA_ChIPseq_BEADSmapq0_rep1.bw GSM2333106 Young_adult NA GSE87524 whole body young adults, LIN-13 ChIP N2 LIN-13 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. LIN-13_YA_rep2 bw_0_1_2_4_ce10 GSM2333106_LIN13_YA_ChIPseq_BEADSmapq0_rep2.bw GSM2333105 Young_adult NA GSE87524 whole body young adults, LIN-13 ChIP N2 LIN-13 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. LIN-13_YA_rep1 bw_0_1_2_4_ce10 GSM2333105_LIN13_YA_ChIPseq_BEADSmapq0_rep1.bw GSM2333104 Young_adult NA GSE87524 whole body young adults, LET-418 ChIP N2 LET-418 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. LET-418_YA_rep2 bw_0_1_2_4_ce10 GSM2333104_LET418_YA_ChIPseq_BEADSmapq0_rep2.bw GSM2333103 Young_adult NA GSE87524 whole body young adults, LET-418 ChIP N2 LET-418 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. LET-418_YA_rep1 bw_0_1_2_4_ce10 GSM2333103_LET418_YA_ChIPseq_BEADSmapq0_rep1.bw GSM2333102 Young_adult NA GSE87524 whole body young adults, HPL-2 ChIP N2 HPL-2 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. HPL-2_YA_rep2 bw_0_1_2_4_ce10 GSM2333102_HPL2_YA_ChIPseq_BEADSmapq0_rep2.bw GSM2333101 Young_adult NA GSE87524 whole body young adults, HPL-2 ChIP N2 HPL-2 ChIP-Seq WS220 Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace. HPL-2_YA_rep1 bw_0_1_2_4_ce10 GSM2333101_HPL2_YA_ChIPseq_BEADSmapq0_rep1.bw GSM2304908 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_hrde-1_GFP_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304907 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_met-2set-25set-32_GFP_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304906 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_met-2set-25_GFP_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304905 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_set-32_GFP_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304904 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_WT_GFP_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304898 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_hrde-1_oma-1_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304897 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_met-2set-25set-32_oma-1_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304896 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_met-2set-25_oma-1_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304895 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_set-32_oma-1_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2304894 Young_adult NA GSE86517 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. Pol II_ChIP-seq_WT_oma-1_RNAi bd_0_1_2_6_ce10 UsingSRR GSM2233445 Young_adult NA GSE84419 whole animal staged young adult (YA) from YL529 (LET-607-GFP transgenic strain) YA YL529 GFP ChIP-Seq WS220 FASTQ files were processed and mapped using BWA (Li et al., 2009), retaining only high quality alignments (Q ¡Ý 30). LET-607 ChIP in staged YA rep 2 bd_0_1_2_6_ce10 UsingSRR GSM2233444 Young_adult NA GSE84419 whole animal staged young adult (YA) from YL529 (LET-607-GFP transgenic strain) YA YL529 GFP ChIP-Seq WS220 FASTQ files were processed and mapped using BWA (Li et al., 2009), retaining only high quality alignments (Q ¡Ý 30). LET-607 ChIP in staged YA rep 1 bd_0_1_2_6_ce10 UsingSRR GSM2155071 Young_adult NA GSE81523 whole animal young adults young adults AM1061 POLR2A ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of Pol II in YA animals at 34¡ãC, replicate 2 bd_0_1_2_6_ce10 UsingSRR GSM2155070 Young_adult NA GSE81523 whole animal young adults young adults AM1061 POLR2A ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of Pol II in YA animals at 34¡ãC, replicate 1 bd_0_1_2_6_ce10 UsingSRR GSM2155069 Young_adult NA GSE81523 whole animal young adults young adults AM1061 POLR2A ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of Pol II in YA animals at 20¡ãC, replicate 2 bd_0_1_2_6_ce10 UsingSRR GSM2155068 Young_adult NA GSE81523 whole animal young adults young adults AM1061 POLR2A ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of Pol II in YA animals at 20¡ãC, replicate 1 bd_0_1_2_6_ce10 UsingSRR GSM2155067 Young_adult NA GSE81523 whole animal young adults young adults AM1061 GFP ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of HSF-1 in YA animals at 34¡ãC, replicate 2 bd_0_1_2_6_ce10 UsingSRR GSM2155066 Young_adult NA GSE81523 whole animal young adults young adults AM1061 GFP ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of HSF-1 in YA animals at 34¡ãC, replicate 1 bd_0_1_2_6_ce10 UsingSRR GSM2155065 Young_adult NA GSE81523 whole animal young adults young adults AM1061 GFP ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of HSF-1 in YA animals at 20¡ãC, replicate 2 bd_0_1_2_6_ce10 UsingSRR GSM2155064 Young_adult NA GSE81523 whole animal young adults young adults AM1061 GFP ChIP-Seq ce10 ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014). ChIP-seq of HSF-1 in YA animals at 20¡ãC, replicate 1 bd_0_1_2_6_ce10 UsingSRR GSM2104331 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads RNAPII Ser2p in RNAi rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104330 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads RNAPII Ser2p in RNAi ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104329 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads Total RNAPII in RNAi rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104328 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads Total RNAPII in RNAi ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104327 Young_adult NA GSE79823 Young adults Blumenthal lab ChIP-Seq ce10 We used Galaxy for processing and mapping all reads CstF64 in RNAi rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104326 Young_adult NA GSE79823 Young adults Blumenthal lab ChIP-Seq ce10 We used Galaxy for processing and mapping all reads CstF64 in RNAi rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104325 Young_adult NA GSE79823 Young adults Blumenthal lab ChIP-Seq ce10 We used Galaxy for processing and mapping all reads CstF64 in RNAi ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104324 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads RNAPII Ser2p WT rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104323 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads RNAPII Ser2p WT ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104322 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads Total RNAPII WT rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104321 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads Total RNAPII WT rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104320 Young_adult NA GSE79823 Young adults POLR2A ChIP-Seq ce10 We used Galaxy for processing and mapping all reads Total RNAPII WT ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104319 Young_adult NA GSE79823 Young adults Blumenthal lab ChIP-Seq ce10 We used Galaxy for processing and mapping all reads CstF50 WT rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104318 Young_adult NA GSE79823 Young adults Blumenthal lab ChIP-Seq ce10 We used Galaxy for processing and mapping all reads CstF50 WT ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104317 Young_adult NA GSE79823 Young adults Blumenthal lab ChIP-Seq ce10 We used Galaxy for processing and mapping all reads CstF64 WT rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2104316 Young_adult NA GSE79823 Young adults Blumenthal lab ChIP-Seq ce10 We used Galaxy for processing and mapping all reads CstF64 WT ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM1919647 Young_adult NA GSE74405 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. WT_p15C_G2_rep2_S2ChIP bd_0_1_2_6_ce10 UsingSRR GSM1919646 Young_adult NA GSE74405 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. WT_p15C_G1_rep2_S2ChIP bd_0_1_2_6_ce10 UsingSRR GSM1919645 Young_adult NA GSE74405 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. WT_23C_G6_rep2_S2ChIP bd_0_1_2_6_ce10 UsingSRR GSM1919644 Young_adult NA GSE74405 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. WT_23C_G4_rep2_S2ChIP bd_0_1_2_6_ce10 UsingSRR GSM1919643 Young_adult NA GSE74405 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. WT_23C_G2_rep2_S2ChIP bd_0_1_2_6_ce10 UsingSRR GSM1919642 Young_adult NA GSE74405 Young adult whole animal POLR2A ChIP-Seq WS190 50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7]. WT_15C_G3_rep2_S2ChIP bd_0_1_2_6_ce10 UsingSRR GSM1508785 Young_adult NA GSE61581 CHIP from whole worm extract young adult tdp-1(ok803) tdp1_CHIP-RNAseControl ChIP-Seq ws220 CHIPseq tdp1_CHIP-RNAseControl bd_0_1_2_6_ce10 UsingSRR GSM1508784 Young_adult NA GSE61581 CHIP from whole worm extract young adult tdp-1(ok803) tdp1_CHIP-2 ChIP-Seq ws220 CHIPseq tdp1_CHIP-2 bd_0_1_2_6_ce10 UsingSRR GSM1508783 Young_adult NA GSE61581 CHIP from whole worm extract young adult tdp-1(ok803) tdp1_CHIP-1 ChIP-Seq ws220 CHIPseq tdp1_CHIP-1 bd_0_1_2_6_ce10 UsingSRR GSM1291070 Young_adult NA GSE53412 whole animal staged young adults from OP179 (SNPC-4-GFP transgenic strain) YA 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 ¡Ý 30). SNPC-4 ChIP in staged young adults (1%) bg_0_1_2_4_ce10 GSM1291070_SNPC4_WA_yAd_IP_Rep0.input.subtracted.bedgraph.gz GSM1291069 Young_adult NA GSE53412 whole animal staged young adults from OP179 (SNPC-4-GFP transgenic strain) YA 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 ¡Ý 30). SNPC-4 input in staged young adults (5%) bg_0_1_2_4_ce10 GSM1291069_SNPC4_YA_input_Rep0.density.scaled.bedgraph.gz GSM1291068 Young_adult NA GSE53412 whole animal staged young adults from OP179 (SNPC-4-GFP transgenic strain) YA 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 ¡Ý 30). SNPC-4 ChIP in staged young adults (5%) bg_0_1_2_4_ce10 GSM1291068_SNPC4_YA_IP_Rep0.density.scaled.bedgraph.gz GSM1259391 Young_adult NA GSE52102 whole young adult worm lysates young adult EAP-1 ChIP-Seq WS220 All sequences were mapped to C.elegans genome assembly (WS220) by BOWTIE package (Langmead B,2009) allowing for zero mismatches and removing monoclonal reads (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, 2009) EAP1-null bd_0_1_2_6_ce10 UsingSRR GSM1259385 Young_adult NA GSE52102 whole young adult worm lysates young adult EAP-1 ChIP-Seq WS220 All sequences were mapped to C.elegans genome assembly (WS220) by BOWTIE package (Langmead B,2009) allowing for zero mismatches and removing monoclonal reads (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, 2009) spr-5_G20_rep2_#2 bd_0_1_2_6_ce10 UsingSRR GSM1259384 Young_adult NA GSE52102 whole young adult worm lysates young adult EAP-1 ChIP-Seq WS220 All sequences were mapped to C.elegans genome assembly (WS220) by BOWTIE package (Langmead B,2009) allowing for zero mismatches and removing monoclonal reads (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, 2009) spr-5_G20_rep2_#1 bd_0_1_2_6_ce10 UsingSRR GSM1259382 Young_adult NA GSE52102 whole young adult worm lysates young adult EAP-1 ChIP-Seq WS220 All sequences were mapped to C.elegans genome assembly (WS220) by BOWTIE package (Langmead B,2009) allowing for zero mismatches and removing monoclonal reads (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, 2009) spr-5_G10 bd_0_1_2_6_ce10 UsingSRR GSM1259381 Young_adult NA GSE52102 whole young adult worm lysates young adult EAP-1 ChIP-Seq WS220 All sequences were mapped to C.elegans genome assembly (WS220) by BOWTIE package (Langmead B,2009) allowing for zero mismatches and removing monoclonal reads (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, 2009) WT_rep2_#2 bd_0_1_2_6_ce10 UsingSRR GSM1259380 Young_adult NA GSE52102 whole young adult worm lysates young adult EAP-1 ChIP-Seq WS220 All sequences were mapped to C.elegans genome assembly (WS220) by BOWTIE package (Langmead B,2009) allowing for zero mismatches and removing monoclonal reads (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, 2009) WT_rep2_#1 bd_0_1_2_6_ce10 UsingSRR GSM1259379 Young_adult NA GSE52102 whole young adult worm lysates young adult EAP-1 ChIP-Seq WS220 All sequences were mapped to C.elegans genome assembly (WS220) by BOWTIE package (Langmead B,2009) allowing for zero mismatches and removing monoclonal reads (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, 2009) WT_rep1 bd_0_1_2_6_ce10 UsingSRR GSM1256808 Young_adult NA GSE51983 Snyder Pmex-5 HPL-2 eGFP YL472 yAd ChIP Rep.2 Young adult YL472(official name : YL472 genotype : unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : It is actually extrachromosomal line by bombardment. made_by : Michelle Kudron in Reinke lab ) Snyder Pmex-5 HPL-2 eGFP YL472 yAd 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 Snyder Pmex-5 HPL-2 eGFP YL472 yAd C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1256808_Snyder_Pmex-5_HPL-2_YL472_yAd_GFP_rep_3_110311_SPADE_00061_FC634TY_L4_TGCT.bedgraph.gz GSM1256806 Young_adult NA GSE51983 Snyder Pmex-5 HPL-2 eGFP YL472 yAd ChIP Rep.1 Young adult YL472(official name : YL472 genotype : unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : It is actually extrachromosomal line by bombardment. made_by : Michelle Kudron in Reinke lab ) Snyder Pmex-5 HPL-2 eGFP YL472 yAd 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 Snyder Pmex-5 HPL-2 eGFP YL472 yAd C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1256806_Snyder_Pmex-5_HPL-2_YL472_yAd_GFP_rep_2_110311_SPADE_00061_FC634TY_L4_ACGT.bedgraph.gz GSM1217544 Young_adult NA GSE50336 seq-SDQ5421_CEC7_fem2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ5421_CEC7_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ5421_CEC7_fem2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217544_CW101_peaks.GFF3.gz GSM1217542 Young_adult NA GSE50335 seq-SDQ5413_CEC7_fem2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ5413_CEC7_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ5413_CEC7_fem2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217542_CW100_peaks.GFF3.gz GSM1217524 Young_adult NA GSE50330 seq-SDQ2382_him5_fem2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ2382_him5_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2382_him5_fem2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217524_BC304_peaks.GFF3.gz GSM1217523 Young_adult NA GSE50330 seq-SDQ2382_him5_fem2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ2382_him5_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2382_him5_fem2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217523_BC292_peaks.GFF3.gz GSM1217500 Young_adult NA GSE50324 seq-SDQ0809_COH1_fem2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ0809_COH1_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0809_COH1_fem2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217500_SDQ0809_COH-1_csr1_peaks.GFF3.gz GSM1217499 Young_adult NA GSE50324 seq-SDQ0809_COH1_fem2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ0809_COH1_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0809_COH1_fem2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217499_BC281_peaks.GFF3.gz GSM1217492 Young_adult NA GSE50322 seq-SDQ3914_REC8_fem2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3914_REC8_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3914_REC8_fem2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217492_SDQ3914_REC8_csr3_peaks.GFF3.gz GSM1217491 Young_adult NA GSE50322 seq-SDQ3914_REC8_fem2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3914_REC8_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3914_REC8_fem2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217491_BC279_peaks.GFF3.gz GSM1217488 Young_adult NA GSE50321 seq-SDQ0802_REC8_fem2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ0802_REC8_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0802_REC8_fem2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217488_BC298_peaks.GFF3.gz GSM1217487 Young_adult NA GSE50321 seq-SDQ0802_REC8_fem2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ0802_REC8_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0802_REC8_fem2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217487_BC278_peaks.GFF3.gz GSM1217484 Young_adult NA GSE50320 seq-G0655G0656_HTP3_fem2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-G0655G0656_HTP3_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-G0655G0656_HTP3_fem2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217484_BC295_peaks.GFF3.gz GSM1217483 Young_adult NA GSE50320 seq-G0655G0656_HTP3_fem2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-G0655G0656_HTP3_fem2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-G0655G0656_HTP3_fem2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217483_BC276_peaks.GFF3.gz GSM1217452 Young_adult NA GSE50312 seq-Ab8895_H3K4me1_fem2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) H3K4me1 ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-Ab8895_H3K4me1_fem2_AD_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1217451 Young_adult NA GSE50312 seq-Ab8895_H3K4me1_fem2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) H3K4me1 ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-Ab8895_H3K4me1_fem2_AD_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1217400 Young_adult NA GSE50299 seq-SDQ4625_T09A5.8_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ4625_T09A5.8_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4625_T09A5.8_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217400_T09A5.8_Q4625_5_19_sequence_peaks.GFF3.gz GSM1217399 Young_adult NA GSE50299 seq-SDQ4625_T09A5.8_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ4625_T09A5.8_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4625_T09A5.8_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217399_T09A5.8_Q4625_5_11_sequence_peaks.GFF3.gz GSM1217352 Young_adult NA GSE50287 seq-WA30534799_H3K4me1_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) H3K4me1 ChIP-Seq WS220 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-WA30534799_H3K4me1_FEM2_AD_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1217351 Young_adult NA GSE50287 seq-WA30534799_H3K4me1_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) H3K4me1 ChIP-Seq WS220 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-WA30534799_H3K4me1_FEM2_AD_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1217348 Young_adult NA GSE50286 seq-WA30335199_H3Ser10_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-WA30335199_H3Ser10_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-WA30335199_H3Ser10_FEM2_AD_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1217347 Young_adult NA GSE50286 seq-WA30335199_H3Ser10_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-WA30335199_H3Ser10_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-WA30335199_H3Ser10_FEM2_AD_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1217344 Young_adult NA GSE50285 seq-SDQ4713_HIM3_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ4713_HIM3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4713_HIM3_FEM2_AD_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1217343 Young_adult NA GSE50285 seq-SDQ4713_HIM3_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ4713_HIM3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4713_HIM3_FEM2_AD_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1217340 Young_adult NA GSE50284 seq-SDQ4498_HIM3_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ4498_HIM3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4498_HIM3_FEM2_AD_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1217338 Young_adult NA GSE50283 seq-SDQ4068_MRG1_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ4068_MRG1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4068_MRG1_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217338_SDQ4068_MRG-1_csr3_peaks.GFF3.gz GSM1217337 Young_adult NA GSE50283 seq-SDQ4068_MRG1_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ4068_MRG1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4068_MRG1_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217337_SDQ4068_MRG1_csr2_peaks.GFF3.gz GSM1217334 Young_adult NA GSE50282 seq-SDQ3989_ASH2_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3989_ASH2_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3989_ASH2_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217334_ACD118_peaks.GFF3.gz GSM1217333 Young_adult NA GSE50282 seq-SDQ3989_ASH2_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3989_ASH2_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3989_ASH2_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217333_ACD117_peaks.GFF3.gz GSM1217330 Young_adult NA GSE50281 seq-SDQ3972_COH3_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3972_COH3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3972_COH3_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217330_SDQ3972_COH3_csr7_peaks.GFF3.gz GSM1217329 Young_adult NA GSE50281 seq-SDQ3972_COH3_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3972_COH3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3972_COH3_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217329_BC277_peaks.GFF3.gz GSM1217326 Young_adult NA GSE50280 seq-SDQ3965_ZIM1_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3965_ZIM1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3965_ZIM1_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217326_SDQ3965_ZIM1_csr5_peaks.GFF3.gz GSM1217325 Young_adult NA GSE50280 seq-SDQ3965_ZIM1_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3965_ZIM1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3965_ZIM1_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217325_SDQ3965_ZIM1_csr4_peaks.GFF3.gz GSM1217321 Young_adult NA GSE50279 seq-SDQ3956_ZHP3_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3956_ZHP3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3956_ZHP3_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217321_SDQ3956_ZHP3_csr4_peaks.GFF3.gz GSM1217322 Young_adult NA GSE50279 seq-SDQ3956_ZHP3_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3956_ZHP3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3956_ZHP3_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217322_SDQ3956_ZHP3_csr5_peaks.GFF3.gz GSM1217318 Young_adult NA GSE50278 seq-SDQ3953_REC8_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3953_REC8_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3953_REC8_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217318_BC296_peaks.GFF3.gz GSM1217317 Young_adult NA GSE50278 seq-SDQ3953_REC8_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3953_REC8_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3953_REC8_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217317_BC280_peaks.GFF3.gz GSM1217314 Young_adult NA GSE50277 seq-SDQ3949_ZIM3_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3949_ZIM3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3949_ZIM3_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217314_SDQ3949_ZIM3_csr6_peaks.GFF3.gz GSM1217313 Young_adult NA GSE50277 seq-SDQ3949_ZIM3_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3949_ZIM3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3949_ZIM3_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217313_SDQ3949_ZIM3_csr5_peaks.GFF3.gz GSM1217310 Young_adult NA GSE50276 seq-SDQ3948_COH3_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3948_COH3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3948_COH3_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217310_SDQ3948_COH-3_csr7_peaks.GFF3.gz GSM1217309 Young_adult NA GSE50276 seq-SDQ3948_COH3_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3948_COH3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3948_COH3_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217309_BC297_peaks.GFF3.gz GSM1217306 Young_adult NA GSE50275 seq-SDQ3942_KLE2_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3942_KLE2_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3942_KLE2_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217306_SDQ3942_KLE-2_csr4_peaks.GFF3.gz GSM1217304 Young_adult NA GSE50274 seq-SDQ3927_MRG1_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3927_MRG1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3927_MRG1_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217304_SDQ3927_MRG1_csr3_peaks.GFF3.gz GSM1217302 Young_adult NA GSE50273 seq-SDQ3925_ZHP3_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3925_ZHP3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3925_ZHP3_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217302_SDQ3925_ZHP3_csr7_peaks.GFF3.gz GSM1217301 Young_adult NA GSE50273 seq-SDQ3925_ZHP3_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3925_ZHP3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3925_ZHP3_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217301_SDQ3925_ZHP3_csr6_peaks.GFF3.gz GSM1217298 Young_adult NA GSE50272 seq-SDQ3907_CHD3_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3907_CHD3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3907_CHD3_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217298_SDQ3907_CHD3_csr3_peaks.GFF3.gz GSM1217297 Young_adult NA GSE50272 seq-SDQ3907_CHD3_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3907_CHD3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3907_CHD3_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217297_SDQ3907_CHD-3_csr1_peaks.GFF3.gz GSM1217294 Young_adult NA GSE50271 seq-SDQ3866_MRE11_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3866_MRE11_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3866_MRE11_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217294_SDQ3866_MRE-11_csr11_peaks.GFF3.gz GSM1217293 Young_adult NA GSE50271 seq-SDQ3866_MRE11_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3866_MRE11_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3866_MRE11_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217293_SDQ3866_MRE11_csr9_peaks.GFF3.gz GSM1217290 Young_adult NA GSE50270 seq-SDQ3853_MSH5_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3853_MSH5_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3853_MSH5_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217290_BC302_peaks.GFF3.gz GSM1217289 Young_adult NA GSE50270 seq-SDQ3853_MSH5_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3853_MSH5_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3853_MSH5_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217289_BC284_peaks.GFF3.gz GSM1217286 Young_adult NA GSE50269 seq-SDQ3849_CHD3_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3849_CHD3_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3849_CHD3_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217286_SDQ3849_CHD3_csr3_peaks.GFF3.gz GSM1217284 Young_adult NA GSE50268 seq-SDQ2366_MRE11_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ2366_MRE11_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2366_MRE11_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217284_SDQ2366_MRE-11_csr7_peaks.GFF3.gz GSM1217283 Young_adult NA GSE50268 seq-SDQ2366_MRE11_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ2366_MRE11_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2366_MRE11_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217283_SDQ2366_MRE11_csr6_peaks.GFF3.gz GSM1217280 Young_adult NA GSE50267 seq-SDQ2356_MRE11_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ2356_MRE11_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2356_MRE11_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217280_SDQ2356_MRE-11_csr5_peaks.GFF3.gz GSM1217279 Young_adult NA GSE50267 seq-SDQ2356_MRE11_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ2356_MRE11_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2356_MRE11_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217279_SDQ2356_MRE11_csr6_peaks.GFF3.gz GSM1217276 Young_adult NA GSE50266 seq-SDQ0835_SCC1_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ0835_SCC1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0835_SCC1_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217276_SDQ0835_SCC-1_csr10_peaks.GFF3.gz GSM1217242 Young_adult NA GSE50257 seq-SDQ0811_RAD51_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ0811_RAD51_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0811_RAD51_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217242_SDQ0811_RAD51_chip_rep2_peaks.GFF3.gz GSM1217241 Young_adult NA GSE50257 seq-SDQ0811_RAD51_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ0811_RAD51_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0811_RAD51_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217241_SDQ0811_RAD51_chip_rep1_peaks.GFF3.gz GSM1217238 Young_adult NA GSE50256 seq-SDQ0801_HIM17_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ0801_HIM17_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0801_HIM17_FEM2_AD_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1217237 Young_adult NA GSE50256 seq-SDQ0801_HIM17_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ0801_HIM17_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0801_HIM17_FEM2_AD_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1206413 Young_adult NA GSE49750 seq-SDQ3898_KLE2_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ3898_KLE2_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3898_KLE2_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1206413_SDQ3898_KLE-2_csr6_peaks.GFF3.gz GSM1206412 Young_adult NA GSE49750 seq-SDQ3898_KLE2_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ3898_KLE2_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3898_KLE2_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1206412_SDQ3898_KLE-2_csr5_peaks.GFF3.gz GSM1206405 Young_adult NA GSE49748 seq-SDQ2972_HIM8_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ2972_HIM8_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2972_HIM8_FEM2_AD_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1206404 Young_adult NA GSE49748 seq-SDQ2972_HIM8_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ2972_HIM8_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2972_HIM8_FEM2_AD_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1206401 Young_adult NA GSE49747 seq-SDQ1665_1666_MRG1_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ1665_1666_MRG1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ1665_1666_MRG1_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1206401_SDQ1665-1666_MRG-1_csr2_peaks.GFF3.gz GSM1206400 Young_adult NA GSE49747 seq-SDQ1665_1666_MRG1_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ1665_1666_MRG1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ1665_1666_MRG1_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1206400_SDQ1665_1666_MRG1_csr1_peaks.GFF3.gz GSM1206397 Young_adult NA GSE49746 seq-SDQ0821_SCC1_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ0821_SCC1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0821_SCC1_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1206397_SDQ0821_SCC-1_csr11_peaks.GFF3.gz GSM1206395 Young_adult NA GSE49745 seq-SDQ0812_COH1_FEM2_AD_ChIP_Rep2 Germline containing young adult fem-2(b245) seq-SDQ0812_COH1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0812_COH1_FEM2_AD_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1206395_SDQ0812_COH-1_csr1_peaks.GFF3.gz GSM1206394 Young_adult NA GSE49745 seq-SDQ0812_COH1_FEM2_AD_ChIP_Rep1 Germline containing young adult fem-2(b245) seq-SDQ0812_COH1_FEM2_AD_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0812_COH1_FEM2_AD_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1206394_BC299_peaks.GFF3.gz GSM1183856 Young_adult NA GSE48756 NFYA-1_GFP_YA_ChIP_Rep2 Young adult OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ) Snyder_NFYA-1_GFP_YA_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NFYA-1_GFP_YA_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183856_Snyder_NFYA-1_GFP_YA_GFP_rep_2_120214_SPADE_00139_FC63BFR_L7_CATT.bedgraph.gz GSM1183854 Young_adult NA GSE48756 NFYA-1_GFP_YA_ChIP_Rep1 Young adult OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ) Snyder_NFYA-1_GFP_YA_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NFYA-1_GFP_YA_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183854_Snyder_NFYA-1_GFP_YA_GFP_rep_1_120214_SPADE_00139_FC63BFR_L7_GTAT.bedgraph.gz GSM1183832 Young_adult NA GSE48750 F23B12.7_GFP_YA_ChIP_Rep2 Young adult OP429(official name : OP429 genotype : unc-119(ed3) III; wgIs429(F23B12.7::TY1GFP-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 F23B12.7::EGFP fusion protein is expressed in the correct F23B12.7 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F23B12.7 transcription factor. made_by : Unknown ) Snyder_F23B12.7_GFP_YA_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_F23B12.7_GFP_YA_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183832_Snyder_F23B12.7_GFP_YA_GFP_rep_2_120216_SPADE_00140_FC63BFJ_L7_TGCT.bedgraph.gz GSM1183830 Young_adult NA GSE48750 F23B12.7_GFP_YA_ChIP_Rep1 Young adult OP429(official name : OP429 genotype : unc-119(ed3) III; wgIs429(F23B12.7::TY1GFP-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 F23B12.7::EGFP fusion protein is expressed in the correct F23B12.7 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F23B12.7 transcription factor. made_by : Unknown ) Snyder_F23B12.7_GFP_YA_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_F23B12.7_GFP_YA_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183830_Snyder_F23B12.7_GFP_YA_GFP_rep_1_120216_SPADE_00140_FC63BFJ_L7_ACGT.bedgraph.gz GSM1076696 Young_adult NA GSE44015 Snyder_LIN-35_GFP_yA_rep2_GFP_TGCT Young adult YL402(official name : YL402 genotype : unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the pie-1 promoter. made_by : Michelle Kudron in Reinke lab ) Snyder_LIN-35_GFP_yA_GFP_TGCT,ChIP DNA ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_LIN-35_GFP_yA_rep2_GFP_TGCT bg_0_1_2_4_ce10 GSM1076696_Snyder_Ppie-1_LIN-35_YL402_yAd_rep2-1.bedgraph.gz GSM1076695 Young_adult NA GSE44015 Snyder_LIN-35_GFP_yA_rep1_GFP_TGCT Young adult YL402(official name : YL402 genotype : unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the pie-1 promoter. made_by : Michelle Kudron in Reinke lab ) Snyder_LIN-35_GFP_yA_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_LIN-35_GFP_yA_rep1_GFP_TGCT bg_0_1_2_4_ce10 GSM1076695_Snyder_Ppie-1_LIN-35_YL402_yAd_rep1-1.bedgraph.gz GSM928331 Young_adult NA GSE37800 Snyder_Ppie1_DPL1_GFP_YA_rep2 Young Adult YL390(official name : YL390 genotype : unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ) Snyder_Ppie1_DPL1_GFP_YA extraction2_seq1 aliquote 1,ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_Ppie1_DPL1_GFP_YA_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928330 Young_adult NA GSE37800 Snyder_Ppie1_DPL1_GFP_YA_rep1 Young Adult YL390(official name : YL390 genotype : unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ) Snyder_Ppie1_DPL1_GFP_YA extraction1_seq1 aliquote 1,ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_Ppie1_DPL1_GFP_YA_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928327 Young_adult NA GSE37799 Snyder_Ppie1_EFL1_GFP_YA_rep2 Young Adult YL445(official name : YL445 genotype : unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ) Snyder_Ppie1_EFL1_GFP_YA extraction2_seq1 aliquote 1,ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_Ppie1_EFL1_GFP_YA_rep2 extraction2_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM928326 Young_adult NA GSE37799 Snyder_Ppie1_EFL1_GFP_YA_rep1 Young Adult YL445(official name : YL445 genotype : unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ) Snyder_Ppie1_EFL1_GFP_YA extraction1_seq1 aliquote 1,ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_Ppie1_EFL1_GFP_YA_rep1 extraction1_seq1 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729307 Young_adult NA GSE29463 Snyder_W03F9.2_GFP_YA_rep2 extraction4_seq4 channel_1 L4-Young Adult OP215(official name : OP215 genotype : unc119(ed3);wgIs215(W03F9.2::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The W03F9.2::EGFP fusion protein is mainly expressed in germline cells. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the W03F9.2 transcription factor. made_by : Tony Hyman's lab from MPI-CBG ) Snyder_W03F9.2_GFP_YA extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_W03F9.2_GFP_YA_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM729306 Young_adult NA GSE29463 Snyder_W03F9.2_GFP_YA_rep1 extraction3_seq3 channel_1 L4-Young Adult OP215(official name : OP215 genotype : unc119(ed3);wgIs215(W03F9.2::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The W03F9.2::EGFP fusion protein is mainly expressed in germline cells. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the W03F9.2 transcription factor. made_by : Tony Hyman's lab from MPI-CBG ) Snyder_W03F9.2_GFP_YA extraction3_seq3 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_W03F9.2_GFP_YA_rep1 extraction3_seq3 aliquote 1 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 GSM700197 Young_adult NA GSE25799 Snyder_PHA-4_GFP_YA_rep1 extraction7_seq7 channel_1 Young Adult OP37(official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ) Snyder_PHA-4_GFP_YA extraction7_seq7 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_PHA-4_GFP_YA_rep1 extraction7_seq7 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700196 Young_adult NA GSE25799 Snyder_PHA-4_GFP_YA_rep1 extraction6_seq6 channel_1 Young Adult OP37(official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ) Snyder_PHA-4_GFP_YA extraction6_seq6 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_PHA-4_GFP_YA_rep1 extraction6_seq6 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700195 Young_adult NA GSE25799 Snyder_PHA-4_GFP_YA_rep2 extraction5_seq5 channel_1 Young Adult OP37(official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ) Snyder_PHA-4_GFP_YA extraction5_seq5 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_PHA-4_GFP_YA_rep2 extraction5_seq5 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM700194 Young_adult NA GSE25799 Snyder_PHA-4_GFP_YA_rep2 extraction4_seq4 channel_1 Young Adult OP37(official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ) Snyder_PHA-4_GFP_YA extraction4_seq4 aliquote 1,channel ch1 is ChIP DNA ChIP-Seq WS180 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_PHA-4_GFP_YA_rep2 extraction4_seq4 aliquote 1 bd_0_1_2_6_ce10 UsingSRR GSM677650 Young_adult NA GSE25794 Snyder_N2_POLII_YA_rep2 extraction2_seq1 channel_2 Young Adult 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_YA_rep2 extraction2_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR GSM677648 Young_adult NA GSE25794 Snyder_N2_POLII_YA_rep1 extraction1_seq1 channel_2 Young Adult 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_YA_rep1 extraction1_seq1 aliquote 2 bd_0_1_2_6_ce10 UsingSRR GSM389650 Young_adult NA GSE15567 daf-16 transgenic worm TJ356 L4/young adult TJ356 POLR2A ChIP-Seq Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp. DAF-16 L4/Young adult replicate 2 POL II bd_0_1_2_6_ce10 UsingSRR GSM389647 Young_adult NA GSE15567 daf-16 transgenic worm TJ356 L4/young adult TJ356 POLR2A ChIP-Seq Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp. DAF-16 L4/Young adult replicate 1 POL II bd_0_1_2_6_ce10 UsingSRR GSM389312 Young_adult NA GSE15535 ama-1 transgenic worm OP34 L4/young adult OP34 POLR2A ChIP-Seq Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp. ama-1 L4/young adult replicate 2 POL II bd_0_1_2_6_ce10 UsingSRR GSM389309 Young_adult NA GSE15535 ama-1 transgenic worm OP34 L4/young adult OP34 POLR2A ChIP-Seq Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp. ama-1 L4/young adult replicate 1 POL II bd_0_1_2_6_ce10 UsingSRR