Illumina Genome Analyzer II sequencing; Glucocorticoid receptor profiling in IMR90,K562 and U2OS (ChIP-seq)
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous
Attributes by original data submitter
Sample
ENA first public
2015-02-26
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA3271458
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
2015-02-26T17:03:02Z
INSDC last update
2018-03-08T20:58:04Z
INSDC status
public
Submitter Id
E-MTAB-2955:K562_GR_chip-seq
broker name
ArrayExpress
cell line
K562
common name
human
sample name
E-MTAB-2955:K562_GR_chip-seq
Sequenced DNA Library
library_name
K562_GR_chip-seq
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were treated with 0.01% ethanol vehicle or 1 μM dexamethasone for 1 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 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.