|
Status |
Public on Jun 11, 2014 |
Title |
snf2-null - nucleosomes 1 |
Sample type |
SRA |
|
|
Source name |
Saccharomyces cerevisiae
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
strain: YDC188 genotype/variation: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ISW1-FL3-KanMX snf2-delta::URA3
|
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 Genome Analyzer II |
|
|
Description |
Biological replicate 1
|
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) |
clarkda@mail.nih.gov
|
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 |
GPL9377 |
Series (1) |
GSE49512 |
Genome-wide nucleosome maps for wild type and Rsc8-depleted Saccharomyces cerevisiae |
|
Relations |
BioSample |
SAMN02299547 |
SRA |
SRX331004 |