biostudies-arrayexpressSophie ShawSaccharomyces cerevisiaehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-9787Genome-wide binding of the histone chaperone Rtt106 was analysed by ChIP-seq. Rtt106 binding was analysed in WT and the mutant backgrounds lacking transcription factors Pdr1 and Pdr3, the HIR histone chaperone subunit Hir1, or the boundary protein Yta7. Two biological replicates had been submitted. mRNA profiles in WT and the mutants lacking Rtt106, Pdr1, Pdr3 or the SWI/SNF subunit Snf2 were analysed by RNA-seq. mRNA profiles in those yeast cells grown in rich media (YPD) and in the glucose-starved condition (YEP) and in response to ketoconazole (YEP+ket) were analysed. Three biological samples for each condition had been submitted.biostudies-arrayexpressSample Collection - For RNA-seq, cells were collected by centrifugation at 11,000 x g for 1 min.Sequencing - Libraries were sequenced using the High Output 1X75 kit on the Illumina NextSeq 500 platform producing 75 bp single end reads.Nucleic Acid Extraction - For RNA-seq, cells were disrupted using a bead beater and then total RNA was prepared using Macherey-Nagel NucleoSpin RNA column according to the manufacturer’s protocol.Library Construction - Sequencing libraries were prepared using the NEBNext Ultra II library preparation kit as per manufacturer's instructions.Sample Collection - For ChIP-seq analyses, collected cells were fixed with 1% formaldehyde at room temperature for 30 min and then at 4 degrees celsius overnight with gently shaking. The cells were then washed in PBS, resuspended in lysis buffer and disrupted using a bead beater. Chromatin was sheared by sonication using a Bioruptor. The target protein-chromatin complex was immunoprecipitated using anti-HA antibody and Dynabeads Protein G.Sequencing - Libraries were sequenced using a High Output 1x75 bp flow cell on an Illumina NextSeq 500 instrument.Growth Protocol - For ChIP-seq and RNA-seq analyses, cells were cultivated in YPD at 30 degrees celsius and collected when they were in log phase growth. For ketoconazole treatment, cells grown in YPD overnight were pelleted and washed with water, resuspended in YEP to an OD600 of 0.6, incubated for 24 hours at 30 degrees celsius, and then treated with 40 uM ketoconazole for 15 min at 30 degrees celsius.Library Construction - ERCC (External RNA Controls Consortium) spike in controls (Baker et al., 2005) were added to the RNA samples to be used as internal controls. Libraries were prepared with the Illumina TruSeq Stranded mRNA kit as per manufacturer's instructions.Nucleic Acid Extraction - For ChIP-seq, the immunoprecipitated protein-chromatin complex was first treated with 1% SDS in TE, incubated overnight at 65 degrees celsius to reverse the crosslinking and then treated with RNase A and proteinase K. DNA was then cleaned using a Qiagen PCR purification kit.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Raw reads were taken and filtered with TrimGalore! using a phred quality score of -q 30. ERCC reads were removed by alignment to the ERCC reference genome using HISAT2. Cleaned reads were then aligned to the S. cerevisiae reference genome using HISAT2. Alignments were processed using SAMtools. Reads were quantified at gene locations using featureCounts with the parameter to split multi-mapping maps across all alignments.Sequence Alignment - Using the Galaxy web interface, sequence reads from fastq files were mapped against the latest version of the yeast genome sacCer3 using BWA. Non-uniquely mapped reads were removed by filtering out all reads with mapping quality less than 20 using SAMtools Filter. To view read coverage distribution across the genome, BAM files were converted into bigwig format.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500ChIP-seqSaccharomyces cerevisiaeSophie ShawVladislav NikolovTakashi KubotafalseSWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genesGenome-wide binding of the histone chaperone Rtt106 was analysed by ChIP-seq. Rtt106 binding was analysed in WT and the mutant backgrounds lacking transcription factors Pdr1 and Pdr3, the HIR histone chaperone subunit Hir1, or the boundary protein Yta7. Two biological replicates had been submitted. mRNA profiles in WT and the mutants lacking Rtt106, Pdr1, Pdr3 or the SWI/SNF subunit Snf2 were analysed by RNA-seq. mRNA profiles in those yeast cells grown in rich media (YPD) and in the glucose-starved condition (YEP) and in response to ketoconazole (YEP+ket) were analysed. Three biological samples for each condition had been submitted.2022-02-21T00:00:00Z2022-05-18T12:20:48.888Z2022-02-04T09:09:30.446ZE-MTAB-9787ERP125222EFO_0002944EFO_0004170EFO_0003789EFO_0002692EFO_0004917EFO_0005518EFO_0004184