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

source_name
A549 cells treated with 100 nM Dexamethasone
cell line
A549
agent
dex
chip antibody
anti-GR (Santa Cruz Biotechnology, sc-1003)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each replicate, 2 ×10^7 nuclei were re-suspended in 1 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS at pH 7.4). Samples were sonicated using a Diagenode Bioruptor XL sonicator at 4°C to fragment chromatin to 200-500 bp segments. Insoluble components were removed by centrifugation for 15 min at 15000 rpm. We conjugated 5 µg of anti-GR to 200 µl of sheep anti-rabbit IgG magnetic beads (Life Technologies). Sheared chromatin in RIPA was then added to the antibody-conjugated beads and incubated on a rotator overnight at 4°C. After incubation, beads were washed five times with a LiCl wash buffer (100 mM Tris at pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate), and remaining ions were removed with a single wash with 1 mL of TE (10 mM Tris-HCl at pH 7.5, 0.1 mM Na2EDTA) at 4°C. Chromatin and antibodies were eluted from beads by incubating for 1 h at 65°C in IP elution buffer (1% SDS, 0.1 M NaHCO3), followed by incubating overnight at 65°C to reverse formaldehyde cross-links. DNA was purified using MinElute DNA purification columns (Qiagen). Illumina TruSeq adapted libraries were constructed using an Apollo 324 NGS Library Prep System with a PrepX Complete ILMN DNA Library Kit (WaferGen Biosystems Inc). ChIP products were amplified with 15 cycles of PCR, and fragments 150-700 bp in length were selected using an AxyPrep MAG PCR Clean-Up Kit (Axygen MAG-PCRCL-50). Libraries were sequenced using single end 50 bp reads on an Illumina HiSeq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
19852640
Reads aligned (%)
178.4
Duplicates removed (%)
7.7
Number of peaks
341 (qval < 1E-05)

hg38

Number of total reads
19852640
Reads aligned (%)
181.3
Duplicates removed (%)
7.6
Number of peaks
560 (qval < 1E-05)

Base call quality data from DBCLS SRA