|
| Status |
Public on Jul 17, 2013 |
| Title |
Wild type -nucleosomes - Repeat |
| 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 HiSeq 2000 |
| |
|
| Description |
gel-purified nucleosomal DNA (MNase)
78-2
|
| 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) |
[email protected]
|
| 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 |
SRX244342 |
| BioSample |
SAMN01924464 |
