Illumina HiSeq 2500 paired end sequencing; Genome-wide profiling of Glucocorticoid receptor binding in A549, Nalm-6, MEF WT and MEF GCN5/PCAF double knockout (ChIP-seq)
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast
Attributes by original data submitter
Sample
ENA first public
2016-11-10
ENA last update
2016-09-22
ENA-CHECKLIST
ERC000011
External Id
SAMEA4462129
INSDC center alias
Institut de Biologie de l'Ecole Normale Superieure
INSDC center name
Institut de Biologie de l'Ecole Normale Superieure
INSDC first public
2016-11-10T17:08:24Z
INSDC last update
2016-09-22T16:57:16Z
INSDC status
public
Submitter Id
E-MTAB-5113:MEF_WT_GR_chip-seq
broker name
ArrayExpress
cell line
MEF
common name
house mouse
genotype
wild type genotype
sample name
E-MTAB-5113:MEF_WT_GR_chip-seq
Sequenced DNA Library
library_name
MEF_WT_GR_chip-seq_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were grown in DMEM supplemented with 10% FBS. Cells were treated with 0.01% ethanol vehicle or 1 μM dexamethasone for 1.5 hour. Cells were cross-linked by adding formaldehyde to a final concentration of 1% and subsequent incubation 3 minutes at room temperature before quenching the reaction by adding glycine to a final concentration of 125 mM. Chromatin was sheared with a Bioruptor water bath sonicator (Diagenode) to produce fragments of ∼100-200 bp. Protein G-coupled magnetic beads (dynabeads, Invitrogen) were preincubated for one and a half hour with GR-antibody (N499) before chromatin was added and incubated for an additional 2-4 h while rotating at 4°C. Subsequently, beads were washed 4 times with 10mM Tris-HCl pH 8.0, 1mM EDTA, 500 mM NaCl, 5% Glycerol, 0.1% Sodium deoxycholate, 0.1% SDS, 1% Triton X-100, 0.5 mg/μl BSA followed by 4 additional washes with 20mM Tris, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate.