|
| Status |
Public on Nov 09, 2015 |
| Title |
Rpb3 ChIP-seq (+SM) Experiment 1; BY4741 |
| Sample type |
SRA |
| |
|
| Source name |
S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
genotype: MATa his3delta1 leu2delta met15delta ura3delta
|
| Growth protocol |
All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 30 min to induce Gcn4, or without adding SM (no SM).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In ChIP-seq experiments, cells were cross-linked with formaldehyde before harvesting. In MNase-seq experiments, nuclei were prepared from unfixed yeast cells and then digested with MNase. Mono-nucleosomal DNA was gel-purified (~150 bp). See paper for details. The antibodies used in this study are anti-H3 antibody from Abcam (Cat#ab1791) and anti-Rpb3 antibody from NeoClone (Cat# W0012)
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH03_4
|
| Data processing |
Paired-end sequences of immunoprecipited DNA or nucleosomal DNA were aligned to the yeast genome (SacCer2) using Bowtie2 with default settings.
Histone H3 and Rpb3 occupancies profiles were created using custom perl programs.
The processed data (bigWig files) were converted from the fastq files supplied here. Analysis of the aligned reads were size-selected as described in the article.
The .bw files for the Rpb3 samples include only unique read pairs.
length used in AGH0*.bw files: range: 120 - 160 bp
Genome_build: SacCer2
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Nov 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alan G. Hinnubusch |
| E-mail(s) |
ahinnebusch@nih.gov
|
| Phone |
301-496-4480
|
| Organization name |
NICHD
|
| Street address |
6 Center Dr. Bldg 6, Rm 230
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE74787 |
Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation |
|
| Relations |
| BioSample |
SAMN04251336 |
| SRA |
SRX1423711 |
