NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1087280 Query DataSets for GSM1087280
Status Public on Jul 17, 2013
Title Brf1 - IP -repeat
Sample type SRA
 
Source name yeast cells
Organism Saccharomyces cerevisiae
Characteristics strain: DDY1389(W303)
genotype: MATalpha ADE2 can1 his3 leu2 lys2delta trp1 ura3 BRF1:3XFLAG:KanMX
antibody: anti-FLAG
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 HiSeq 2000
 
Description Immuno-purified MNase digested DNA
415-IP-2
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
E-mail(s) nagarajavel@yahoo.com
Organization name National Institutes of Health
Department NICHD
Lab PGD
Street address 9500 Rockville Pike, Buld 6A/Rm 2A14
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platform ID GPL13821
Series (1)
GSE44586 Genome-wide nucleosome, TFIIIC and TFIIIB occupancies in Saccharomyces cerevisiae
Relations
SRA SRX244352
BioSample SAMN01924474

Supplementary file Size Download File type/resource
GSM1087280_Brf1-IP-2.bw 5.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap