GSM2829780 Asynchronous_cell NA GSE106104 100% S. cerevisiae cells ChIPseq 6408 asynchronous Pk9 ChIP rep2 6411 - SMC4 tagged with Pk9 Scer_6408_Async_Pk9ChIP ChIP-Seq SacCer3 ChIP-seq: mapping: Mapping was conducted using bowtie version 1.2 to the SK1 Liti version. Mapping parameters used are:-p 8 -q -m 1 -v 0 -S. ChIPseq_Scer_6408_Async_Pk9ChIP_rep2 bd_0_1_2_6_sc3 UsingSRR GSM2829778 Asynchronous_cell NA GSE106104 100% S. cerevisiae cells ChIPseq 6408 asynchronous Pk9 ChIP rep1 6409 - SMC4 tagged with Pk9 Scer_6408_Async_Pk9ChIP ChIP-Seq SacCer3 ChIP-seq: mapping: Mapping was conducted using bowtie version 1.2 to the SK1 Liti version. Mapping parameters used are:-p 8 -q -m 1 -v 0 -S. ChIPseq_Scer_6408_Async_Pk9ChIP_rep1 bd_0_1_2_6_sc3 UsingSRR GSM1707631 Asynchronous_cell NA GSE69696 asynchronous cells SBY10483 psh1 pGAL-Flag-Cse4 strain Flag-Cse4 ChIP ChIP-Seq SacCer3 Illumina Real Time Analysis and CASAVA software used for base-calling psh1 pGAL-Flag-Cse4 strain Flag-Cse4 ChIP bd_0_1_2_non_sc3 GSM1707631_SBY10483_psh1pGALFlagCse4_ChIP_MonoNucsOnlyPeaks.bed.gz GSM1707630 Asynchronous_cell NA GSE69696 asynchronous cells SBY10483 MNase-Seq SacCer3 Illumina Real Time Analysis and CASAVA software used for base-calling psh1 pGAL-Flag-Cse4 strain input DNA bd_0_1_2_non_sc3 GSM1707630_SBY10483_psh1pGALFlagCse4_input_MonoNucsOnlyPeaks.bed.gz GSM1707629 Asynchronous_cell NA GSE69696 asynchronous cells SBY10425 pGAL-Flag-Cse4 strain Flag-Cse4 ChIP ChIP-Seq SacCer3 Illumina Real Time Analysis and CASAVA software used for base-calling pGAL-Flag-Cse4 strain Flag-Cse4 ChIP bd_0_1_2_non_sc3 GSM1707629_SBY10425_pGALFlagCse4_ChIP_MonoNucsOnlyPeaks.bed.gz GSM1707628 Asynchronous_cell NA GSE69696 asynchronous cells SBY10425 MNase-Seq SacCer3 Illumina Real Time Analysis and CASAVA software used for base-calling pGAL-Flag-Cse4 strain input DNA bd_0_1_2_non_sc3 GSM1707628_SBY10425_pGALFlagCse4_input_MonoNucsOnlyPeaks.bed.gz GSM1707627 Asynchronous_cell NA GSE69696 asynchronous cells SBY10484 psh1 Flag-Cse4 strain Flag-Cse4 ChIP ChIP-Seq SacCer3 Illumina Real Time Analysis and CASAVA software used for base-calling psh1 Flag-Cse4 strain Flag-Cse4 ChIP bd_0_1_2_non_sc3 GSM1707627_SBY10484_psh1FlagCse4_ChIP_MonoNucsOnlyPeaks.bed.gz GSM1707626 Asynchronous_cell NA GSE69696 asynchronous cells SBY10484 MNase-Seq SacCer3 Illumina Real Time Analysis and CASAVA software used for base-calling psh1 Flag-Cse4 strain input DNA bd_0_1_2_non_sc3 GSM1707626_SBY10484_psh1FlagCse4_input_MonoNucsOnlyPeaks.bed.gz GSM1707625 Asynchronous_cell NA GSE69696 asynchronous cells SBY10419 Flag-Cse4 strain Flag-Cse4 ChIP ChIP-Seq SacCer3 Illumina Real Time Analysis and CASAVA software used for base-calling Flag-Cse4 strain Flag-Cse4 ChIP bd_0_1_2_non_sc3 GSM1707625_SBY10419_FlagCse4_ChIP_MonoNucsOnlyPeaks.bed.gz GSM1707624 Asynchronous_cell NA GSE69696 asynchronous cells SBY10419 MNase-Seq SacCer3 Illumina Real Time Analysis and CASAVA software used for base-calling Flag-Cse4 strain input DNA bd_0_1_2_non_sc3 GSM1707624_SBY10419_FlagCse4_input_MonoNucsOnlyPeaks.bed.gz GSM1904282 Asynchronous_cell NA GSE69065 rat1-1 cells grown at 37C Asynchronous culture rat1-1[YIW138] UM185 , gift from Steve Bell lab ChIP-Seq sacCer3 Data were aligned to the May 2008 build of the S. cerevisiae genome: using BOWTIE2 rat1-1_MCM_ChIP_37C bd_0_1_2_6_sc3 UsingSRR GSM1904281 Asynchronous_cell NA GSE69065 rat1-1 cells grown at 24C Asynchronous culture rat1-1[YIW138] UM185 , gift from Steve Bell lab ChIP-Seq sacCer3 Data were aligned to the May 2008 build of the S. cerevisiae genome: using BOWTIE2 rat1-1_MCM_ChIP_24C bd_0_1_2_6_sc3 UsingSRR GSM1904280 Asynchronous_cell NA GSE69065 rat1-1 cells grown at 37C Asynchronous culture rat1-1[YIW138] 1108 , gift from Steve Bell lab ChIP-Seq sacCer3 Data were aligned to the May 2008 build of the S. cerevisiae genome: using BOWTIE2 rat1-1_ORC_ChIP_37C bd_0_1_2_6_sc3 UsingSRR GSM1904279 Asynchronous_cell NA GSE69065 rat1-1 cells grown at 24C Asynchronous culture rat1-1[YIW138] 1108 , gift from Steve Bell lab ChIP-Seq sacCer3 Data were aligned to the May 2008 build of the S. cerevisiae genome: using BOWTIE2 rat1-1_ORC_ChIP_24C bd_0_1_2_6_sc3 UsingSRR GSM1868510 Asynchronous_cell NA GSE73145 Budding yeast cells Asynchronous POLR2A ChIP-Seq sacCer3 Fastq files were put through the FASTQC program to verify good quality of library Pol2_IP_WT_2 bw_0_1_2_4_sc3 GSM1868510_1089-2_bamCoverage.bigwig GSM1868509 Asynchronous_cell NA GSE73145 Budding yeast cells Asynchronous POLR2A ChIP-Seq sacCer3 Fastq files were put through the FASTQC program to verify good quality of library Pol2_IP_WT_1 bw_0_1_2_4_sc3 GSM1868509_1089-1_bamCoverage.bigwig GSM1402303 Asynchronous_cell NA GSE53420 asynchronous cells BY4741:MATa his3жд1 leu2жд0 met15жд0 ura3жд0 RNA/DNA hybrid ChIP-Seq sacCer3 ChIP-seq reads were aligned to the sacCer3 genome assembly using novoalign V2.07 with the option -r Random Batch2_ChIP-seq_Wild-type bw_0_1_2_4_sc3 GSM1402303_Batch2_ChIP-seq_Wild-type_normalized.bw GSM1402299 Asynchronous_cell NA GSE53420 asynchronous cells BY4741:MATa his3жд1 leu2жд0 met15жд0 ura3жд0 RNA/DNA hybrid ChIP-Seq sacCer3 ChIP-seq reads were aligned to the sacCer3 genome assembly using novoalign V2.07 with the option -r Random Batch1_ChIP-seq_Wild-type bw_0_1_2_4_sc3 GSM1402299_Batch1_ChIP-seq_Wild-type_normalized.bw GSM832693 Asynchronous_cell NA GSE33704 Rpb3-chIP-seq Asynchronous WT Asynchronous WT Rpb3-chIP-seq Asynchronous 2 ChIP-Seq sacCer3 Reads were mapped allowing 2 mismatches to the S. cerevisiae genome (release r.64). Reads were then binned into 50 bp bins and quantile normalized across experiments. Rpb3-chIP-seq Asynchronous WT 2 bd_0_1_2_6_sc3 UsingSRR GSM832692 Asynchronous_cell NA GSE33704 Rpb3-chIP-seq Asynchronous WT Asynchronous WT Rpb3-chIP-seq Asynchronous 1 ChIP-Seq sacCer3 Reads were mapped allowing 2 mismatches to the S. cerevisiae genome (release r.64). Reads were then binned into 50 bp bins and quantile normalized across experiments. Rpb3-chIP-seq Asynchronous WT 1 bd_0_1_2_6_sc3 UsingSRR GSM424491 Asynchronous_cell NA GSE16926 WT W303 MNase Mapview alignment files were generated with the program MAQ, which was fed the raw data in the Illumina fastq format, and a build of the S. cerevisiae S288C from SGD (released 12/16/2005). All of the default options were used, except that the maximum number of allowed mismatches was raised to 3. All further processed data was generated using in-house analysis methods described in the GSE16926_nucleosomes_2009_supp.pdf. WT_Asynchronous_23C_Nucleosomes bd_0_1_2_6_sc3 UsingSRR GSM3069971 Asynchronous_cell NA GSE112465 Asynchronous growth in liquid YPD MNase Align with tophat: $ tophat2 -p 4 -G ~/GenomeIndex/Saccharomyces_cerevisiae.EF4.65.gtf -I 200 -o tophat_out ~/GenomeIndex/yeast *R1_merged.fastq *R2_merged.fastq MNase_YPD30_WT-B_166_40U.sgr.gz bd_0_1_2_6_sc3 UsingSRR GSM3069970 Asynchronous_cell NA GSE112465 Asynchronous growth in liquid YPD MNase Align with tophat: $ tophat2 -p 4 -G ~/GenomeIndex/Saccharomyces_cerevisiae.EF4.65.gtf -I 200 -o tophat_out ~/GenomeIndex/yeast *R1_merged.fastq *R2_merged.fastq MNase_YPD30_WT-B_166_20U.sgr.gz bd_0_1_2_6_sc3 UsingSRR GSM3069962 Asynchronous_cell NA GSE112465 Asynchronous growth in liquid YPD MNase Align with tophat: $ tophat2 -p 4 -G ~/GenomeIndex/Saccharomyces_cerevisiae.EF4.65.gtf -I 200 -o tophat_out ~/GenomeIndex/yeast *R1_merged.fastq *R2_merged.fastq MNase_YPD23_WT-A_166_40U.sgr.gz bd_0_1_2_6_sc3 UsingSRR GSM3069956 Asynchronous_cell NA GSE112465 Asynchronous growth in liquid YPD POLR2A ChIP-Seq Align with bowtie: $ bowtie2 -x -U .fastq -S -mapped.sam Pol2_YPD30_WT-B_6916_IP bd_0_1_2_6_sc3 UsingSRR GSM3069954 Asynchronous_cell NA GSE112465 Asynchronous growth in liquid YPD POLR2A ChIP-Seq Align with bowtie: $ bowtie2 -x -U .fastq -S -mapped.sam Pol2_YPD30_WT-A_6915_IP bd_0_1_2_6_sc3 UsingSRR GSM1705338 Asynchronous_cell NA GSE69651 W303 W303 DNase sacCer2 Single-end sequencing reads were aligned with Bowtie 0.12.7 with the following parameters: -n 2 -l 20 -3 30 -m 1 --best --strata DNase-seq_W303_S_cerevisiae_Sample2 bd_0_1_2_6_sc3 UsingSRR GSM1705337 Asynchronous_cell NA GSE69651 W303 W303 DNase sacCer2 Single-end sequencing reads were aligned with Bowtie 0.12.7 with the following parameters: -n 2 -l 20 -3 30 -m 1 --best --strata DNase-seq_W303_S_cerevisiae_Sample1 bd_0_1_2_6_sc3 UsingSRR