Illumina HiSeq 4000 sequencing; Transcription factor binding and epigenetic modifications during NuRD complex induction
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
2018-05-31
ENA last update
2018-05-21
ENA-CHECKLIST
ERC000011
External Id
SAMEA4671572
INSDC center alias
University of Cambridge
INSDC center name
University of Cambridge
INSDC first public
2018-05-31T17:02:01Z
INSDC last update
2018-05-21T17:01:05Z
INSDC status
public
Submitter Id
E-MTAB-6804:24h_H3K4me3_R2
broker name
ArrayExpress
cell type
embryonic stem cell
common name
house mouse
genotype
Mbd3 inducible
sample name
E-MTAB-6804:24h_H3K4me3_R2
strain
129/Ola
Sequenced DNA Library
library_name
24h_H3K4me3_R2_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were maintained on gelatin-coated culture vessels in 2i/LIF, consisting of DMEM:F-12 and Neurobasal media (1:1, Invitrogen) supplemented with N2 (in-house) and B27 (Gibco), L-glutamine and beta-mercaptoethanol, 3μM CHIR99021 and 1μM PD0325901 inhibitors, plus 10ng/ml LIF. Translocation of Mbd3b protein to the nucleus was induced with 4-hydroxytamoxifen added directly to the culture media to a final concentration of 0.4nM for varying times as indicated. Fixation was carried out using 1% formaldehyde 10 minutes at room temperature and quenched with 150 mM glycine. DNA was fragmented in the presence of 0.4% SDS using a Bioruptor sonication instrument (Diagenode) producing a size range of between 200 and 300 bp. Libraries were prepared using the NEXTflex Rapid DNA-seq kit.