Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
IRF2BP2

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293-GR
cell line
HEK293-GR
treatment 1
steroid-depleted medium, 48h
treatment 2
ethanol, 1h
chip antibody
Anti-IRF2BP2 antibody (A303190A, Bethyl laboratories)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, the HEK293-GR cells were grown on 10-cm dishes in charcoal-stripped medium for 2 days, treated with vehicle or dex (100 nM, 1 h), and fixed with 1% (v/v) formaldehyde 10 min at room temperature. Chromatin was fragmented to ∼200–400 bp using sonication (Bioruptor UCD-300, Diagenode). Anti-IRF2BP2 antibody (A303190A, Bethyl laboratories) was coupled to protein-A- beads (Millipore), fragmented chromatin was incubated with antibody-coupled beads overnight, washed, eluted and de-crosslinked in the presence of proteinase K (Fermentas). Chromatin fragments were purified using MinElute columns (Qiagen). Fragmented de-crosslinked chromatin was used as an input control. Library preparation was done using NEBNext Ultra II kit (New England Biolabs) and sequenced using Illumina Hiseq2000 at EMBL GeneCore (Heidelberg, Germany).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
44720178
Reads aligned (%)
76.6
Duplicates removed (%)
16.4
Number of peaks
1000 (qval < 1E-05)

hg38

Number of total reads
44720178
Reads aligned (%)
77.8
Duplicates removed (%)
15.5
Number of peaks
834 (qval < 1E-05)

Base call quality data from DBCLS SRA