Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Lung
Cell type
BEAS-2B
Primary Tissue
Lung
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Cultured Beas-2B airway epithelial cells
antibody
GR
treatment
dexamethasone + TNF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed as described previously described (PMID: 23508109), with the following modifications: cross-linking was performed by adding methanol-free 16% formaldehyde directly to the culture media to a final concentration of 1% and incubating for 5 minutes at room temperature with gentle rocking; samples were subsequently sonicated with a Diagenode Bioruptor at high power in 30-second bursts separated by 30-second incubations in ice water for a total of 34 cycles. GR antibody was a gift of Miles Pufall; RNAP2 antibody was from BioLegend (920101) and the p65 antibody was from Santa Cruz (sc-372x). A minimum of 1 ng DNA from ChIP samples were used to prepare libraries using the Nugen Ovation Ultralow System V2 1-16 Part No. 0344 according to the manufacturer’s instructions. Samples were run on an Illumina HiSeq using 1X50 bp end reads

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
26592898
Reads aligned (%)
83.9
Duplicates removed (%)
14.1
Number of peaks
21982 (qval < 1E-05)

hg38

Number of total reads
26592898
Reads aligned (%)
85.1
Duplicates removed (%)
13.3
Number of peaks
22027 (qval < 1E-05)

Base call quality data from DBCLS SRA