|
| Status |
Public on Jul 17, 2020 |
| Title |
SIR3-EBD G1_estradiol H3K79me3 ChIP rep. 2 |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JRY12170
chip antibody: H3K79me3 (Diagenode C15410068, lot # A86-0023P)
condition: G1 (alpha factor) arrest followed by addition of estradiol for 3 hours
genotype: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78
|
| 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 |
|
| Relations |
| BioSample |
SAMN15567457 |
| SRA |
SRX8754212 |
