GSM3030623 Phase_G1 NA GSE111426 Yeast G1-arrested HA ChIP-Seq saccer3 Fastq files were aligned to saccer3 using BWA SPT16HA6_tp0_rep2_Sonicated_Spt16_IP bd_0_1_2_6_sc3 UsingSRR GSM3030622 Phase_G1 NA GSE111426 Yeast G1-arrested HA ChIP-Seq saccer3 Fastq files were aligned to saccer3 using BWA SPT16HA6_tp0_rep1_Sonicated_Spt16_IP bd_0_1_2_6_sc3 UsingSRR GSM2985380 Phase_G1 NA GSE110286 SPT16HA6 tp0 Sonicated Rpb3 IP G1-arrested Rpb3 ChIP-Seq saccer3 Fastq files were aligned to saccer3 using BWA SPT16HA6 rep2 tp0 Sonicated Rpb3 IP bd_0_1_2_6_sc3 UsingSRR GSM2985379 Phase_G1 NA GSE110286 SPT16HA6 tp0 Sonicated Rpb3 IP G1-arrested Rpb3 ChIP-Seq saccer3 Fastq files were aligned to saccer3 using BWA SPT16HA6 rep1 tp0 Sonicated Rpb3 IP bd_0_1_2_6_sc3 UsingSRR GSM3072006 Phase_G1 NA GSE112522 whole cell G1 MNase sacCer3 Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. y1138: WT G1 input MNase-ssSeq repeat 2 bw_0_1_2_4_sc3 GSM3072006_y1138_minus.bw GSM3072002 Phase_G1 NA GSE112522 whole cell G1 MNase sacCer3 Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. y1232: WT G1 input MNase-ssSeq repeat 1 bw_0_1_2_4_sc3 GSM3072002_y1232_minus.bw GSM2328754 Phase_G1 NA GSE87356 whole cell G1 phase Rfa1 ChIP-Seq sacCer3 After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed WT_RPA-ChIP_G1-phase_rep2 bd_0_1_2_6_sc3 UsingSRR GSM2328753 Phase_G1 NA GSE87356 whole cell G1 phase Rfa1 ChIP-Seq sacCer3 After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed WT_RPA-ChIP_G1-phase_rep1 bd_0_1_2_6_sc3 UsingSRR GSM2705874 Phase_G1 NA GSE101536 whole cell G1 phase MCM6_G1_ChIP ChIP-Seq sacCer3 After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed MCM6_G1_ChIP_rep2 bw_0_1_2_4_sc3 GSM2705874_MGC-r.bw GSM2705868 Phase_G1 NA GSE101536 whole cell G1 phase CDC45_G1_ChIP ChIP-Seq sacCer3 After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed CDC45_G1_ChIP_rep2 bw_0_1_2_4_sc3 GSM2705868_CGC-r.bw GSM2705850 Phase_G1 NA GSE101536 whole cell G1 phase MCM6_G1_ChIP ChIP-Seq sacCer3 After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed MCM6_G1_ChIP_rep1 bw_0_1_2_4_sc3 GSM2705850_MGC.bw GSM2705844 Phase_G1 NA GSE101536 whole cell G1 phase CDC45_G1_ChIP ChIP-Seq sacCer3 After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed CDC45_G1_ChIP_rep1 bw_0_1_2_4_sc3 GSM2705844_CGC.bw GSM2211745 Phase_G1 NA GSE83648 WT_MNase-Seq_G1-phase G1 phase MNase sacCer3 After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed WT_MNase-Seq_G1-phase_rep2 bd_0_1_2_6_sc3 UsingSRR GSM2211744 Phase_G1 NA GSE83648 WT_MNase-Seq_G1-phase G1 phase MNase sacCer3 After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed WT_MNase-Seq_G1-phase_rep1 bd_0_1_2_6_sc3 UsingSRR GSM2350622 Phase_G1 NA GSE88877 Hsp90 temperature-sensitive strain with allele G170D W303 DNase sacCer3 Quality control: fastQC (0.10.1) G170DD15 bd_0_1_2_4_sc3 GSM2350622_G170DD15_mapped.hot.bed.gz GSM1617343 Phase_G1 NA GSE66215 whole cell G1 phase TAP ChIP-Seq sacCer3 ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009). w3031a strain Spt16 ChIP-seq bw_0_1_2_4_sc3 GSM1617343_w3031a_g1_chip.bw GSM1617341 Phase_G1 NA GSE66215 whole cell G1 phase TAP ChIP-Seq sacCer3 ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009). Spt16 TAP tagged ChIP-seq bw_0_1_2_4_sc3 GSM1617341_spt16_tap_g1_chip.bw GSM1617330 Phase_G1 NA GSE66215 whole cell G1 phase MNase sacCer3 ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009). WT T45 MNase-seq_3 bw_0_1_2_4_sc3 GSM1617330_wt_T45_Input_rep3.bw GSM1617329 Phase_G1 NA GSE66215 whole cell G1 phase MNase sacCer3 ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009). WT T45 MNase-seq_2 bw_0_1_2_4_sc3 GSM1617329_wt_T45_Input_rep2.bw GSM1617328 Phase_G1 NA GSE66215 whole cell G1 phase MNase sacCer3 ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009). WT T45 MNase-seq_1 bw_0_1_2_4_sc3 GSM1617328_wt_T45_input.bw GSM1617327 Phase_G1 NA GSE66215 whole cell G1 phase MNase sacCer3 ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009). WT T0 MNase-seq_3 bw_0_1_2_4_sc3 GSM1617327_wt_T0_Input_rep3.bw GSM1617326 Phase_G1 NA GSE66215 whole cell G1 phase MNase sacCer3 ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009). WT T0 MNase-seq_2 bw_0_1_2_4_sc3 GSM1617326_wt_T0_Input_rep2.bw GSM1617325 Phase_G1 NA GSE66215 whole cell G1 phase MNase sacCer3 ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009). WT T0 MNase-seq_1 bw_0_1_2_4_sc3 GSM1617325_wt_T0_input.bw GSM1712303 Phase_G1 NA GSE69907 Saccharomyces cerevisiae and Candida glabrata mixed cells ChIP -of Scc1_PK9 with PK ChIP-Seq SacCer3 Library sequencing was carried out on the Ion Torrent Proton Fig4_G1 Scc1PK9_IP bw_0_1_2_4_sc3 GSM1712303_Fig4_G1_IP.bigwig GSM1272609 Phase_G1 NA GSE52614 whole cell G1 FLAG ChIP-Seq sacCer3 Reads were aligned to the yeast genome (sacCer3) using the Bowtie2 software. Only the consist pair reads were used for the further analysis. G1 Mcm6 protein chip bw_0_1_2_4_sc3 GSM1272609_y61_minus.bw GSM1272607 Phase_G1 NA GSE52614 whole cell G1 FLAG ChIP-Seq sacCer3 Reads were aligned to the yeast genome (sacCer3) using the Bowtie2 software. Only the consist pair reads were used for the further analysis. G1 Mcm4 protein chip bw_0_1_2_4_sc3 GSM1272607_y58_minus.bw GSM1314109 Phase_G1 NA GSE54377 MN_Scerevisiae_WT_G1 MNase-Seq Alignment: bowtie 0.12.7 MN_Scerevisiae_WT_G1 bd_0_1_2_6_sc3 UsingSRR GSM832697 Phase_G1 NA GSE33704 Rpb3-chIP-seq G1 Arrested WT G1-Arrest WT Rpb3-chIP-seq G1 Arrested 2 ChIP-Seq 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 G1 Arrested WT 2 bd_0_1_2_6_sc3 UsingSRR GSM832696 Phase_G1 NA GSE33704 Rpb3-chIP-seq G1 Arrested WT G1-Arrest WT Rpb3-chIP-seq G1 Arrested 1 ChIP-Seq 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 G1 Arrested WT 1 bd_0_1_2_6_sc3 UsingSRR