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Sample GSM1087269 Query DataSets for GSM1087269
Status Public on Jul 17, 2013
Title Wild type - nucleosomes
Sample type SRA
Source name yeast cells
Organism Saccharomyces cerevisiae
Characteristics strain: JRY4013 (W303)
genotype: MATalpha can1-100 his3-11,15 leu2-3, 112 lys2-delta trp1-1 ura3-1
Growth protocol Cells grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium.
Extracted molecule genomic DNA
Extraction protocol Nuclei were digested with micrococcal nuclease. Nucleosomes: mono-nucleosomal DNA was gel-purified. IP experiments: DNA was extracted from a fraction of the MNase digest (Input) for paired-end sequencing. The rest of the digest was immunoprecipitated using anti-FLAG antibody and eluted with 3-FLAG peptide (IP) and the DNA was extracted and sequenced.
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 gel-purified nucleosomal DNA (MNase)
Data processing Nucleosomes: For wild type - experiment, ELAND was used to align the reads to the NCBI Saccharomyces cerevisiae genome sequence Build 2.1
Nucleosomes: For wild type repeat sample, BWA was used to align the reads to Saccharomyces cerevisiae genome sequence
Samples were aligned with either BWA (413-Input, 413-IP, 416-1-Input, 416-1-IP, 415-1-Input, 415-1-IP) or Bowtie 2 (416-1-Input, 416-3-IP, 415-2-Input, 415-2-IP) to the Saccharomyces cerevisiae genome sequence (SacCer2).
Submission date Feb 22, 2013
Last update date May 15, 2019
Contact name Nagarajavel Vivekananthan
Organization name National Institutes of Health
Department NICHD
Street address 9500 Rockville Pike, Buld 6A/Rm 2A14
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
Platform ID GPL9377
Series (1)
GSE44586 Genome-wide nucleosome, TFIIIC and TFIIIB occupancies in Saccharomyces cerevisiae
SRA SRX244341
BioSample SAMN01924463

Supplementary file Size Download File type/resource 25.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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