Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

Alias
E-MTAB-5113:A549_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
ERS1361303
Sample Name
ERS1361303
Title
A549_GR_chip-seq
cell_line
A549
genotype
wild type genotype
organism
Homo sapiens

Sequenced DNA Library

library_name
A549_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
10665315
Reads aligned (%)
15.8
Duplicates removed (%)
29.7
Number of peaks
1529 (qval < 1E-05)

hg38

Number of total reads
10665315
Reads aligned (%)
16.3
Duplicates removed (%)
29.0
Number of peaks
1550 (qval < 1E-05)

Base call quality data from DBCLS SRA