|
| Status |
Public on Jun 11, 2014 |
| Title |
Wild type -nucleosomes 1500U |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: MCY3647
genotype/variation: MATalpha his3-delta-200 lys2-801 leu2-3,112 ura3-52
treatment: digested with 1500U MNase
|
| Growth protocol |
All strains were grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium, except MCY3860, which was grown in galactose and then switched to glucose, in which it arrested at OD ~ 0.8 (due to depletion of the essential Rsc8/Swh3 protein)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were digested with micrococcal nuclease. Mono-nucleosomal DNA was gel-purified.
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 |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Biological replicate 2 (digested with 1500U MNase)
|
| Data processing |
Nucleosome sequences were aligned to the yeast genome (SacCer2) using Bowtie2.
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.
|
| |
|
| Submission date |
Aug 02, 2013 |
| 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) |
| GSE49512 |
Genome-wide nucleosome maps for wild type and Rsc8-depleted Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN02299542 |
| SRA |
SRX331003 |
