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Sample GSM4675925 Query DataSets for GSM4675925
Status Public on Jul 17, 2020
Title sir3∆ sonication input rep. 2
Sample type SRA
Source name Saccharomyces cerevisiae
Organism Saccharomyces cerevisiae
Characteristics strain: JRY12168
chip antibody: None
condition: Cycling
genotype: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; sir3{delta}
Treatment protocol For SIR3-EBD cultures, estradiol was used at 50 µM. "No estradiol" samples were grown with 0.5% ethanol (solvent control). For G1 arrests, 10 nM alpha factor was added. For G2/M arrests, 15 µg/mL nocodazole was added.
Growth protocol Yeast were cultured at 37° in YPD.
Extracted molecule genomic DNA
Extraction protocol Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented using either sonication (all H3K79me3 samples) or MNase (all Sir4-myc and Sir3-EBD samples except for a subset fragmented by sonication, noted in the sample title). DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiniSeq
Data processing For samples sequenced on the Illumina NovaSeq 6000, FASTQ generation was performed using Illumina Casava v2.2. For samples sequenced on the Illumina Miniseq, FASTQ generation was performed using the Generate FASTQ module of Illumina Local Run Manager
Raw reads were mapped to SacCer3 genome modified to include hml∆::HML* and mat∆ using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were generated from aligned reads and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA). For MNase samples, only reads between 130-180 bp (mononucleosome) were included in bedgraphs.
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: bedgraph (normalized to genome-wide median)
Submission date Jul 17, 2020
Last update date Jul 18, 2020
Contact name Davis Goodnight
Organization name UC Berkeley
Department Molecular & Cell Biology
Lab Rine
Street address 440 Barker Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platform ID GPL22715
Series (1)
GSE150737 S-phase independent silencing establishment in Saccharomyces cerevisiae
BioSample SAMN15567468
SRA SRX8754201

Supplementary file Size Download File type/resource
GSM4675925_JRY12168-in_0_500_median_normalized.bedgraph.gz 64.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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