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Sample GSM1200256 Query DataSets for GSM1200256
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
Phone 3014966966
Organization name NICHD, NIH
Department DDB
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
BioSample SAMN02299547
SRA SRX331004

Supplementary file Size Download File type/resource 35.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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