Otx2 ChIP-seq in Rex1GFPd2 mouse embryonic stem cell line
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA
Attributes by original data submitter
Sample
ENA first public
2014-06-24
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2612444
INSDC center alias
University of Manchester
INSDC center name
University of Manchester
INSDC first public
2014-06-24T17:01:43Z
INSDC last update
2018-03-08T17:11:02Z
INSDC status
public
Submitter Id
E-MTAB-2281:OTX2_4hr
broker name
ArrayExpress
cell line
Rex1GFPd2
cell type
embryonic stem cell
common name
house mouse
sample name
E-MTAB-2281:OTX2_4hr
sex
male
Sequenced DNA Library
library_name
OTX2_4hr
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Rex1GFPd2 mouse ES cells were maintained in NDiff N2B27 media in the presence of CHIR99021 and PD0325901 as described in Yang et al., 2012. For time series of differentiation, the media containing inhibitor was removed and replaced with NDiff N2B27 media as time lindicated. ES cells were cross-linked as described in Lee et al., 2006. Yang SH, Kalkan T, Morrisroe C, Smith A, Sharrocks AD. (2012) PLoS Genet. 2012;8(12):e1003112. A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation. Lee TI, Johnstone SE, Young RA. (2006) Nat Protoc. 1(2):729-48. Chromatin immunoprecipitation and microarray-based analysis of protein location. ChIP-seq was performed as described in Lee et al., 2006, with the following modifications. The crosslinked material was sheared by water bath sonication using bio-rupter for 16 mins, at high level, 30 secs on/ 30 secs off, 4 ⁰C. The size of sheared DNA fragments was between 100 bp to 500 bp, with median size around 300 bp. Immunoprecipitation was performed by incubating 1.5×107cells with 2.5 µg of Otx2 antibodies (ProteinTech Group, Inc; 13497-1-AP) cross-linked to dynabeads protein A (Invitrogen), overnight at 4 ⁰C. Lee TI, Johnstone SE, Young RA. (2006) Nat Protoc. 1(2):729-48. Chromatin immunoprecipitation and microarray-based analysis of protein location.