|
| Status |
Public on Jan 03, 2014 |
| Title |
Cdx2_ChIPseq_ZHBTc4-TSC |
| Sample type |
SRA |
| |
|
| Source name |
ZHBTc4-TS cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
antibody: Cdx2 (CDX2-88, BioGenex)
|
| Growth protocol |
TS cells were maintained in GMEM/10% FBS supplemented with 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on MEF feeders.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sheared into fragments with an average size of 300-500 bp using a Covaris S220.
Sequencing libraries were prepared from ChIP DNA using KAPA Library Amplification Kit (KAPA Biosystem). Briefly, ChIP DNA was end-repaired, A-tailed, ligated to the adapters, size selected to 200-500 bp and amplified by PCR. Libraries were sequenced on the HiSeq 1500 (Illumina) as single-end 50-bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
On MEF feeders, with FGF4/heparin/Activin A
|
| 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 |
Oct 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Itoshi NIKAIDO |
| E-mail(s) |
itoshi.nikaido@riken.jp
|
| 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 |
GPL13112 |
| Series (2) |
| GSE28455 |
Sox2-regulatory networks in embryonic and trophoblast stem cells |
| GSE51511 |
ChIP-seq anlysis of Sox2, Tfap2c, and Cdx2 in trophoblast stem cells. |
|
| Relations |
| BioSample |
SAMN02566988 |
| SRA |
SRX404307 |
