GSM3040133: tSH2Δ mutant Rep1 ATAC; Saccharomyces cerevisiae; ATAC-seq
For ATAC seq: Five million wild-type (S288C) and spt6-tSH2Δ cell were collected during their linear phase of growth. Three replicates each were collected for the wild type and mutant (total of 6 samples). ATAC-seq libraries were made as described (Buenrostro et al., 2015; Schep et al., 2017), with the exception of a double-sided SPRI bead size selection step of each library, using 0.5x and 1x ratio of SPRI beads to obtain a library size range of ~150 bp to ~2 kb.For RNAseq:  RNA was extracted from 10 million cells using acid phenol extraction method followed by DNAse treatment before subjecting it to library preparation. For RNA-seq:  RNA was extracted from 10 million cells using acid-phenol extraction method followed by DNAse treatment before subjecting it to library preparation. For ATAC-seq: WT replicates were index labelled using Ad2.1_TAAGGCGA, Ad2.2_CGTACTAG, and Ad2.3_AGGCAGAA Illumina indexes, while the mutant libraries were indexed using Ad2.6_TAGGCATG, Ad2.7_CTCTCTAC, and Ad2.8_CAGAGAGG (Buenrostro 2013). All 6 libraries were combined and sequenced on a single lane of Illumina Hiseq 2500 using v4 chemistry for 50bp paired-end output. For RNA-seq: WT and spt6-tSH2Δ strains were cultured in YPD for 4 hours after diluting overnight saturated cultures to an OD600 of 0.2. RNA was extracted from the cells using acid-phenol method as described. Residual DNA was eliminated using DNase treatments (DNAse I, Ambion Cat #AM2222). Library preparation and sequencing were performed at the High-Throughput Sequencing Facility (HTSF) at UNC-Chapel Hill. Libraries were prepared using TruSeq Stranded Total RNA with RiboZero Gold Library Prep Kit (Illumina) and were sequenced using Illumina HiSeq 2500 (50 bp, single-end reads).