Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Blood
Cell type
NALM-6
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

Alias
E-MTAB-5113:Nalm-6_GR_chip-seq
Broker name
ArrayExpress
Description
Protocols: Cells were grown in DMEM supplemented with 10% FBS. Approximately 10 million cells were treated with 0.01% ethanol vehicle or 1 uM dexamethasone for 1.5 h. Chromatin was sheared with a Bio-ruptor water bath sonicator (Diagenode) to produce fragments of 100-200 bp. Protein-G coupled magnetic beads (Active- Motif) were preincubated for 1 h with GR-antibody (N499) before chromatin was added and incubated for an additional 2-4 h while rotating at 4C. Subsequently beads were washed three times with 10 mM TrisaHCl pH 8.0, 1 mM EDTA, 500 mM NaCl, 5% (vol/vol) glycerol, 0.1% sodium deoxycholate, 0.1% SDS, 1% Triton X-100, 0.5 mg/uL BSA, followed by three additional washes with 20 mM Tris, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% Nonidet P-40, and 0.5% sodium deoxycholate.
ENA checklist
ERC000011
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
SRA accession
ERS1361305
Sample Name
ERS1361305
Title
Nalm-6_GR_chip-seq
cell_line
NALM6
genotype
wild type genotype
organism
Homo sapiens

Sequenced DNA Library

library_name
Nalm-6_GR_chip-seq_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were grown in DMEM supplemented with 10% FBS. Approximately 10 million cells were treated with 0.01% ethanol vehicle or 1 uM dexamethasone for 1.5 h. Chromatin was sheared with a Bio-ruptor water bath sonicator (Diagenode) to produce fragments of 100-200 bp. Protein-G coupled magnetic beads (Active- Motif) were preincubated for 1 h with GR-antibody (N499) before chromatin was added and incubated for an additional 2-4 h while rotating at 4C. Subsequently beads were washed three times with 10 mM TrisaHCl pH 8.0, 1 mM EDTA, 500 mM NaCl, 5% (vol/vol) glycerol, 0.1% sodium deoxycholate, 0.1% SDS, 1% Triton X-100, 0.5 mg/uL BSA, followed by three additional washes with 20 mM Tris, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% Nonidet P-40, and 0.5% sodium deoxycholate.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
7663500
Reads aligned (%)
62.5
Duplicates removed (%)
16.1
Number of peaks
9471 (qval < 1E-05)

hg38

Number of total reads
7663500
Reads aligned (%)
63.2
Duplicates removed (%)
15.8
Number of peaks
9520 (qval < 1E-05)

Base call quality data from DBCLS SRA