Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
MOLM-1
NA
NA

Attributes by original data submitter

Sample

ENA first public
2014-04-03
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2335245
INSDC center alias
ERASMUSMC
INSDC center name
Erasmus MC, University Medical Center Rotterdam
INSDC first public
2014-04-03T17:00:38Z
INSDC last update
2018-03-08T17:07:58Z
INSDC status
public
Submitter Id
E-MTAB-2224:MOLM1_BRD4
broker name
ArrayExpress
cell line
MOLM-1
cell type
myeloblast
chromosome aberration
3q-aberration
common name
human
genotype
wild type
sample name
E-MTAB-2224:MOLM1_BRD4
sex
female
specimen with known storage state
frozen specimen

Sequenced DNA Library

library_name
MOLM-1 extract 8
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell lines were cultured using media conditions as follows. MUTZ-3: 60% alpha-MEM (Life Technologies), 20% FBS (PAA), 20% conditioned medium of cell line 5637, and 10 ng/ml hrGM-CSF (Amgen); K562, MOLM-1, and U937: 90% RPMI and 10% FBS. All cultures contained 50 U/ml penicillin and 50 μg/ml streptomycin (Sigma). JQ1 sensitivity was measured by mitochondrial dehydrogenase (MTT assay) after 6, 24, 48, and 72 h of exposure with JQ1 (5, 50, 500, or 1,000 nM) or vehicle control (DMSO, 0.05%). The cell line MOLM1 was treated for 6 hours with 1,000 nM of JQ1. Subsequently, a BRD4 Chip-Seq was performed on these cells to determine the effect of JQ1 treatment of enhancers and super enhancers. Immunoprecipitated material was de-crosslinked and was amplified using a Whole Genome Amplification kit (WGA2/WGA3; Sigma-Aldrich, Zwijndrecht, The Netherlands). Subsequently, the fragments were sheared by a Covaris shearing device (Covaris S2) and size selected by an agrose gel. ChIP experiments were performed as previously described (Bindels et al., 2012; doi: http://dx.doi.org/10.1182/blood-2011-11-393827). Immunoprecipitation of cross-linked chromatin was performed with antibodies directed against Histone H3K4me1, H3K4me3, H3K27ac, p300, and BRD4, or an equal amount of isotype IgG as background control. Three independent experiments were performed and the amount of immunoprecipitated DNA was represented relative to cross-linked input DNA.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
192465714
Reads aligned (%)
98.8
Duplicates removed (%)
25.2
Number of peaks
3841 (qval < 1E-05)

hg19

Number of total reads
192465714
Reads aligned (%)
98.0
Duplicates removed (%)
26.8
Number of peaks
2695 (qval < 1E-05)

Base call quality data from DBCLS SRA