|
| Status |
Public on Aug 20, 2015 |
| Title |
Input DNA Drpd3 log 2 |
| Sample type |
SRA |
| |
|
| Source name |
Δrpd3 log
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: W303
genotype/variation: delta-rpd3
isolate number: isolate 2
conditions of harvest: log cells
|
| Treatment protocol |
Cells were fixed with 1% formaldehyde for 20 minutes
|
| Growth protocol |
log cells were grown to OD600 0.4 to 0.6; DS cells were harvested 2 hours after glucose exhaustion; Q cells were purified from 7-day stationary phase cultures with a Percoll gradient; thiolutin (3 ug/mL final) or rapamycin (100 nM) was added to log cells for 1 hour at OD600=0.6 prior to crosslinking and ChIP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were disrupted with glass beads then crosslinked DNA was sonicated to generate ~300 bp fragments.
Libraries were constructed using NuGEN Ovation UltraLow Library systems
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2 on very sensitive mode
Genome_build: Saccharomyces_cerevisia.EF4.65
|
| |
|
| Submission date |
Mar 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey N McKnight |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oregon
|
| Department |
Institute of Molecular Biology
|
| Lab |
McKnight Lab
|
| Street address |
1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97408 |
| Country |
USA |
| |
|
| Platform ID |
GPL9134 |
| Series (2) |
| GSE67150 |
Characterization of H3 density, H3 or H4 acetylation, Rpd3 binding, TFIIB binding, and Rpb3 (pol II) binding in wild type and rpd3 cells as they transition from logarithmic growth to diauxic shift to quiescence [ChIP-Seq] |
| GSE67151 |
Rpd3 drives transcriptional quiescence |
|
| Relations |
| BioSample |
SAMN03437091 |
| SRA |
SRX964214 |
