GSM3464154 Embryo_early GSM3464163 GSE122341 early embryo set-25(n5021) III Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_set-25_eemb_20oC_rep3 bd_0_1_2_6_ce10 UsingSRR GSM3464153 Embryo_early GSM3464162 GSE122341 early embryo set-25(n5021) III Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_set-25_eemb_20oC_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3464152 Embryo_early GSM3464161 GSE122341 early embryo set-25(n5021) III Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_set-25_eemb_20oC_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3464151 Embryo_early GSM3464160 GSE122341 early embryo met-2(n4256) III Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_met-2_eemb_20oC_rep3 bd_0_1_2_6_ce10 UsingSRR GSM3464150 Embryo_early GSM3464159 GSE122341 early embryo met-2(n4256) III Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_met-2_eemb_20oC_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3464149 Embryo_early GSM3464158 GSE122341 early embryo met-2(n4256) III Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_met-2_eemb_20oC_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3464148 Embryo_early GSM3464157 GSE122341 early embryo N2 (Bristol) Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_N2_eemb_20oC_rep3 bd_0_1_2_6_ce10 UsingSRR GSM3464147 Embryo_early GSM3464156 GSE122341 early embryo N2 (Bristol) Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_N2_eemb_20oC_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3464146 Embryo_early GSM3464155 GSE122341 early embryo N2 (Bristol) Lem-2 ChIP-Seq ce10 Basecalling was performed using RTA v. 1.13.48. ChIP_lem-2_N2_eemb_20oC_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3187970 Embryo_early NA GSE115709 Mixed stage early embryos N2 wild type MNase WS220 Paired-end MNase-seq reads were mapped to the C. elegans genome (Wormbase version WS220) using Bowtie with default settings. Early embryo MNase-seq rep2 bw_0_1_2_4_ce10 GSM3187970_MNase8.Eembryo4.i4_insert.bigger140_scale.10Mil.Autos.bw GSM3187969 Embryo_early NA GSE115709 Mixed stage early embryos N2 wild type MNase WS220 Paired-end MNase-seq reads were mapped to the C. elegans genome (Wormbase version WS220) using Bowtie with default settings. Early embryo MNase-seq rep1 bw_0_1_2_4_ce10 GSM3187969_MNase4.Eembryo6.i10_insert.bigger140_scale.10Mil.Autos.bw GSM2267045 Embryo_early NA GSE85445 mixed stage early embryos 1cell to 350 cell stage KW2309 AMA-1 ChIP-Seq ws220 bowtie 1.0.1 was run with the -m 2 option to map the Illumina reads to the genome version ws220 KW2309-Sig-7RNAi-1Ama-2-CHIP bg_0_1_2_4_ce10 GSM2267045_AMA1_KW2309.sig7RNAi_r2.bedgraph.gz GSM2267044 Embryo_early NA GSE85445 mixed stage early embryos 1cell to 350 cell stage KW2309 AMA-1 ChIP-Seq ws220 bowtie 1.0.1 was run with the -m 2 option to map the Illumina reads to the genome version ws220 KW2309-Sig-7RNAi-1Ama-1-CHIP bg_0_1_2_4_ce10 GSM2267044_AMA1_KW2309.sig7RNAi_r1.bedgraph.gz GSM2267043 Embryo_early NA GSE85445 mixed stage early embryos 1cell to 350 cell stage KW2309 AMA-1 ChIP-Seq ws220 bowtie 1.0.1 was run with the -m 2 option to map the Illumina reads to the genome version ws220 KW2309-L4440-1Ama-2-CHIP bg_0_1_2_4_ce10 GSM2267043_AMA1_KW2309.L4440_r2.bedgraph.gz GSM2267042 Embryo_early NA GSE85445 mixed stage early embryos 1cell to 350 cell stage KW2309 AMA-1 ChIP-Seq ws220 bowtie 1.0.1 was run with the -m 2 option to map the Illumina reads to the genome version ws220 KW2309-L4440-1Ama-1-CHIP bg_0_1_2_4_ce10 GSM2267042_AMA1_KW2309.L4440_r1.bedgraph.gz GSM1911031 Embryo_early NA GSE74134 Early embryo extracts early embryo GW1 LEM-2 ChIP-Seq ce6 All paired-end ChIP-seq data (2x50bp) were mapped to the c.elegans genome (ce6) with the R package QuasR (http://www.bioconductor.org/packages/3.1/bioc/html/QuasR.html) using the included aligner bowtie [1] allowing only for uniquely mapping read pairs. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6")" which instructs bowtie to align using the parameters "--fr -m 1 --best --strata --maxins 500 --phred33-quals". Read density along the genome was calculated by tiling the genome into 200kb windows (non-overlapping) and counting the number of sequence fragments within each window [lem2_win200k_rawCounts.txt]. The command used to create the window count table was qCount(proj,regions,useRead="first"). This instructs QuasR to position each read at the middle of its respective fragment (determined by the two reads) and to only consider the first read (on any strand) for quantification in order to avoid double counting. To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of mapped reads and multiplied by the average library size. Log2 expression levels were calculated after adding a pseudocount of 1 (y=log2(x+1)) [lem2_win200k_normalized.txt]. lem2_wild-type_2 bd_0_1_2_6_ce10 UsingSRR GSM1911030 Embryo_early NA GSE74134 Early embryo extracts early embryo GW1 LEM-2 ChIP-Seq ce6 All paired-end ChIP-seq data (2x50bp) were mapped to the c.elegans genome (ce6) with the R package QuasR (http://www.bioconductor.org/packages/3.1/bioc/html/QuasR.html) using the included aligner bowtie [1] allowing only for uniquely mapping read pairs. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6")" which instructs bowtie to align using the parameters "--fr -m 1 --best --strata --maxins 500 --phred33-quals". Read density along the genome was calculated by tiling the genome into 200kb windows (non-overlapping) and counting the number of sequence fragments within each window [lem2_win200k_rawCounts.txt]. The command used to create the window count table was qCount(proj,regions,useRead="first"). This instructs QuasR to position each read at the middle of its respective fragment (determined by the two reads) and to only consider the first read (on any strand) for quantification in order to avoid double counting. To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of mapped reads and multiplied by the average library size. Log2 expression levels were calculated after adding a pseudocount of 1 (y=log2(x+1)) [lem2_win200k_normalized.txt]. lem2_wild-type_1 bd_0_1_2_6_ce10 UsingSRR GSM1217536 Embryo_early NA GSE50333 seq-SDQ3927_MRG1_N2_Eemb_ChIP_Rep2 Early Embryo N2 seq-SDQ3927_MRG1_N2_Eemb_ChIP ChIP-Seq ce10 Illumina_DNA_Sequencing:JL:1 protocol. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge. Processed data are obtained using following parameters: read length is 36 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3927_MRG1_N2_Eemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217536_BC238_peaks.GFF3.gz GSM1217540 Embryo_early NA GSE50334 seq-ab817_8WG16_639746_N2_Eemb_ChIP_Rep2 Early Embryo N2 POLR2A ChIP-Seq ce10 Illumina_DNA_Sequencing:JL:1 protocol. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge. Processed data are obtained using following parameters: read length is 36 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-ab817_8WG16_639746_N2_Eemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217540_BC239_ab817_PolII_639746_Eemb18A_mBC046_M6_trimmed_peaks.GFF3.gz GSM1217539 Embryo_early NA GSE50334 seq-ab817_8WG16_639746_N2_Eemb_ChIP_Rep1 Early Embryo N2 POLR2A ChIP-Seq ce10 Illumina_DNA_Sequencing:JL:1 protocol. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge. Processed data are obtained using following parameters: read length is 36 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-ab817_8WG16_639746_N2_Eemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217539_tTE10C_peaks.GFF3.gz GSM1217535 Embryo_early NA GSE50333 seq-SDQ3927_MRG1_N2_Eemb_ChIP_Rep1 Early Embryo N2 seq-SDQ3927_MRG1_N2_Eemb_ChIP ChIP-Seq ce10 Illumina_DNA_Sequencing:JL:1 protocol. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge. Processed data are obtained using following parameters: read length is 36 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3927_MRG1_N2_Eemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217535_TE004_peaks.GFF3.gz GSM1217532 Embryo_early NA GSE50332 seq-SDQ3838_T26A5.5_N2_Eemb_ChIP_Rep2 Early Embryo N2 seq-SDQ3838_T26A5.5_N2_Eemb_ChIP ChIP-Seq ce10 Illumina_DNA_Sequencing:JL:1 protocol. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge. Processed data are obtained using following parameters: read length is 36 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3838_T26A5.5_N2_Eemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217532_seq-SDQ3838_T26A5.5_N2_Eemb_r2_peaks.GFF3.gz GSM1217531 Embryo_early NA GSE50332 seq-SDQ3838_T26A5.5_N2_Eemb_ChIP_Rep1 Early Embryo N2 seq-SDQ3838_T26A5.5_N2_Eemb_ChIP ChIP-Seq ce10 Illumina_DNA_Sequencing:JL:1 protocol. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge. Processed data are obtained using following parameters: read length is 36 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3838_T26A5.5_N2_Eemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217531_seq-SDQ3838_T26A5.5_N2_Eemb_r1_peaks.GFF3.gz GSM1217262 Embryo_early GSM1217260 GSE50262 seq-ab8895_H3K4me1_733246_N2_Eemb_ChIP_Rep2 Early Embryo N2 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_733246_N2_Eemb_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1217261 Embryo_early GSM1217259 GSE50262 seq-ab8895_H3K4me1_733246_N2_Eemb_ChIP_Rep1 Early Embryo N2 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_733246_N2_Eemb_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1206351 Embryo_early GSM1206349 GSE49734 seq-WA30634849_H3K27ac_8002_N2_Eemb_ChIP_Rep2 Early Embryo N2 H3K27ac 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-WA30634849_H3K27ac_8002_N2_Eemb_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1206350 Embryo_early GSM1206348 GSE49734 seq-WA30634849_H3K27ac_8002_N2_Eemb_ChIP_Rep1 Early Embryo N2 H3K27ac 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-WA30634849_H3K27ac_8002_N2_Eemb_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM677626 Embryo_early NA GSE25788 Snyder_N2_POLII_eemb_rep2 extraction2_seq1 channel_2 early embryo N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ) POLR2A ChIP-Seq WS170 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_eemb_rep2 extraction2_seq1 aliquote 2 bd_0_1_2_4_ce4 GSM677626_Snyder_N2_POLII_eemb_rep2.bedgraph.gz GSM677624 Embryo_early NA GSE25788 Snyder_N2_POLII_eemb_rep1 extraction1_seq1 channel_2 early embryo N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ) POLR2A ChIP-Seq WS170 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_eemb_rep1 extraction1_seq1 aliquote 2 bd_0_1_2_4_ce4 GSM677624_Snyder_N2_POLII_eemb_rep1.bedgraph.gz