|
| Status |
Public on Jun 12, 2012 |
| Title |
Wild type |
| Sample type |
SRA |
| |
|
| Source name |
WT_ESCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: Cast/Eij /129/Sv
genotype/variation: wild type
cell type: Embryonic stem cell (ESC)
|
| Treatment protocol |
For ChIP-seq the cells were treated for 3 h with proteasome inhibitor (15uM, MG132, Sigma) before chromatin was cross-linked for 10 min at RT with 1% formaldehyde. The cross-linking reaction was stopped by addition of 0.125 M glycine.
|
| Growth protocol |
Female ESCs expressing V5-tagged REX1 and control wild-type ESCs were grown without feeders to 80% confluence (3·107 cells per ChIP or 1·108 cells per ChIP-seq).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Purified ChIP-DNA was prepared for sequencing on a HiSeq 2000 sequencer using Illumina standerd protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling , Illumina pipeline 1.7.0
Read Alignment, Eland, Illumina pipeline 1.7.0
import, filter, normalize and coverage calculation, using R based bioconductor packages (Shortread and ChIP-Seq packages)
peak calling using using R based bioconductor package(MACS)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
Mar 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Eskeatnaf Mulugeta Achame |
| E-mail(s) |
e.mulugetaachame@erasmusmc.nl
|
| Phone |
0031614883537
|
| URL |
http://www.erasmusmc.nl/rede/
|
| Organization name |
Erasmusmc
|
| Department |
Reproduction and Development
|
| Lab |
Reproduction and Development
|
| Street address |
Dr Molewaterplein 50
|
| City |
Rotterdam |
| State/province |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE36417 |
ChIP-sequencing (ChIP-seq) experiments on female ESCs expressing V5-tagged REX1 and control wild-type Embryonic stem cells (ESCs) |
|
| Relations |
| SRA |
SRX128353 |
| BioSample |
SAMN00810990 |
