|
| Status |
Public on Oct 28, 2014 |
| Title |
439U_Input-1 |
| Sample type |
SRA |
| |
|
| Source name |
Input: HA-H4 (no 3AT) Experiment 2
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YDC439
genotype: MATa ade2-1 leu2-3,112 trp1-1 ura3-1 hht1-hhf1delta::LEU2 URA3::HHT2-HA-HHF2
treatment: no 3-aminotriazole
|
| Treatment protocol |
Formaldehyde-fixed and sonicated
|
| Growth protocol |
All strains were grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium (untreated), or in synthetic complete medium without histidine followed by addition of 10 mM 3AT for 20 min (3AT-induced).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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 |
Biological replicate 1
|
| Data processing |
Nucleosome sequences were aligned to the yeast genome (SacCer2) using Bowtie with default settings.
Nucleosome occupancy maps were created using programs described by Cole et al. (2011) Nucleic Acids Res. 39, 9521-9535.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
The .bw files for the Rpb3 samples include only unique read pairs.
Genome_build: SacCer2
|
| |
|
| Submission date |
Jan 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
David Johannes Clark |
| E-mail(s) |
[email protected]
|
| Phone |
3014966966
|
| Organization name |
NICHD, NIH
|
| Department |
DDB
|
| Lab |
SCGE
|
| Street address |
6 Center Drive Bldg 6A Rm 2A02
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE54524 |
Genome-wide nucleosome, histone and Pol II maps for wild type Saccharomyces cerevisiae induced with 3-aminotriazole (3AT) |
|
| Relations |
| BioSample |
SAMN02602826 |
| SRA |
SRX455431 |
