|
| Status |
Public on Nov 06, 2012 |
| Title |
RNA Polymerase II CTD domain ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Fission yeast cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: 972 h-
develomental stage: No
tap tag: No TAP tag
chip antibody: RNA Polymerase II CTD antibody [CTD(4H8) (Abcam, ab5408)]
|
| Treatment protocol |
No
|
| Growth protocol |
Cells in YEA + 2% glucose were collected in log phase
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed as described previously [Zhu et al., 2006]. RNA Polymerase II CTD antibody is CTD(4H8) (Abcam, ab5408). Libraries were prepared according to Illumina's instructions.DNA-end was repaired to overhang a 3‟-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Bed: Sequence reads were mapped to the ASM294v1 NCBI assembly of the S.pombe genome using Bowtie (version 0.12.7) with default parameters.
Wig: RPM (read per million) counts were calculated from the alignment files and wig files were created with a custom script.
Genome Build:
1-4H8.bed: ASM294v1
1-4H8.rpm.wig: ASM294v1
|
| |
|
| Submission date |
Feb 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Claes M Gustafsson |
| E-mail(s) |
claes.gustafsson@medkem.gu.se
|
| Organization name |
Gothenburg University
|
| Department |
Department of Medical biochemistry and cell biology
|
| Street address |
Medcinaregatan 9A
|
| City |
Gothenburg |
| ZIP/Postal code |
405 30 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE35524 |
Mediator promotes CENP-A incorporation at fission yeast centromeres [ChIP-seq] |
| GSE35527 |
Mediator promotes CENP-A incorporation at fission yeast centromeres |
|
| Relations |
| SRA |
SRX118453 |
| BioSample |
SAMN00780334 |
