|
| Status |
Public on Oct 17, 2013 |
| Title |
Sox2 ChIP-seq, Oct3/4KO Day2 |
| Sample type |
SRA |
| |
|
| Source name |
ZHBTc4 ES cells, +Tet, Day 2
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
cell line: ZHBTc4
treatment: Tet
time: 2 days
chip antibody: Sox2 produced in-house
condition: On MEF feeders, with FGF4/heparin/Activin A
|
| Treatment protocol |
TS cells were induced in GMEM/10% FBS supplemented with 1 ug/ml Tet, 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on MEF feeders.
|
| Growth protocol |
ES cells were maintained in GMEM supplemented with 10% FBS and 1,000 U/ml LIF on gelatin-coated dishes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was enzymatically sheared into fragments with an average size of 300-500 bp using the ChIP-IT Express Enzymatic Kit (Active Motif). Sequencing libraries were prepared from ChIP DNA according to the manufacturer's protocols. Briefly, ChP DNA was end-repaired, A-tailed, ligated to the adapters, size selected to 200-400 bp and amplified by 18 cycles of PCR.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against Sox2
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2. Sequence reads were aligned to the mouse reference genome (mm9) using Bowtie2 with default parameters. Sequence reads overlapping with repetitive sequences were removed using BedTools and repeat region data from UCSC Genome Browse. Peak Calling was performed using MACS2 with input DNA as a control and with a q-value cutoff of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using MACS2. The signals were normalized by sequencing depth of million mapped reads with the --SPMR option.
|
| |
|
| Submission date |
Apr 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Itoshi NIKAIDO |
| E-mail(s) |
[email protected]
|
| Organization name |
RIKEN
|
| Department |
Center for Biosystems Dynamics Research
|
| Lab |
Laboratory for Bioinformatics Research
|
| Street address |
2-1 Hirosawa
|
| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE28453 |
Dynamics of Sox2 and Esrrb occupancy during the differentiation of embryonic stem cells into trophoblast stem cells. |
| GSE28455 |
Sox2-regulatory networks in embryonic and trophoblast stem cells |
|
| Relations |
| SRA |
SRX057757 |
| BioSample |
SAMN00259682 |
