|
Status |
Public on Dec 07, 2015 |
Title |
ChIPseq_Suz12_2i_BR2 |
Sample type |
SRA |
|
|
Source name |
Embryonic stem cells
|
Organism |
Mus musculus |
Characteristics |
developmental stage: E14 chip antibody: Suz12 (Anti-Suz12, ab1207, Abcam)
|
Treatment protocol |
2i mESCs were grown in serum free NDiff 227 supplemented with MEK inhibitor PD0325901 (1µM) and GSK3 inhibitor CHIR99021 (3µM) in presence of LIF.
|
Growth protocol |
All cell-culture was conducted in feeder-free condition.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Libraries were prepared according to Illumina's instructions.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Illumina Casava software 1.8.2 used for basecalling of Hiseq2000 and NextSeq 500 data. Library strategy: ChIP-seq. The reads were aligned to build version mm9 of the mouse genome using bwa (version 0.7.12) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Reads from PCR duplicates were also removed. MACS (version 2.0.10.20130306), was used to identify regions of ChIP-seq enrichment over background using parameters --nomodel --broad. Genome_build: mm9
|
|
|
Submission date |
Aug 18, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Shuang-Yin Wang |
Organization name |
RIMLS
|
Department |
Molecular Biology
|
Street address |
Geert Grooteplein 28
|
City |
Nijmegen |
ZIP/Postal code |
6525GA |
Country |
Netherlands |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE72164 |
Dynamic reorganization of extremely long-range promoter-promoter interactions between two states of pluripotency |
|
Relations |
BioSample |
SAMN03998789 |
SRA |
SRX1158309 |