Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GRHL2

Cell type

Cell type Class
Lung
Cell type
Tracheal epithelial cells
NA
NA

Attributes by original data submitter

Sample

source_name
Bronchial Epithelial Cells
cell type
Bronchial Epithelial Cells
donor
C29
chip antibody
GRHL2
chip antibody manufacturer
Sigma

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
20 million cells were crosslinked for 10 minutes in 1% formaldehyde followed by 5 minutes of quenching in 0.125 M glycine. Cells were then washed with cold PBS pH7.4, and collected in the presence of cold cell lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, and Roche Complete Protease Inhibitor Cocktail Cat #11836145001). Nuclei were pelleted by centrifugation at 2,000 rpm for 5 minutes at 4C, and the supertanant discarded. Sheared chromatin was then prepared by sonicating the nuclei in the presence of RIPA buffer (1 x PBS pH 7.4, 1% NP-40, 0.5% NaDOC, Roche Protease Inhibitor Cocktail), followed by centrifugation to remove cell debris. To collected GRHL2-bound DNA, the chromatin was immunoprecipitated with an anti-GRHL2 antibody (Sigma HPA004820), the formaldehyde crosslinks were reversed by heating overnight at 65C, and the DNA was collected using Qiagen PCR cleanup columns. For input control samples, reverse-crosslinked DNA was isolated from an aliquot of the sonicated but not immunoprecipitated chromatin. DNA ends were blunted using a mixture of Klenow DNA polymerase, T4 DNA polymerase, and T4 polynucleotide kinase (PNK). Three-prime adenine was then added using 3'-5' exo- Klenow fragment, Illumina Y-adapters were ligated using T4 DNA ligase. The ligated DNA was gel size selected for 150-300 bp fragments, and PCR-amplified to make the final sequencing library. Samples were sequenced on an Illumina HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
34448754
Reads aligned (%)
89.4
Duplicates removed (%)
6.5
Number of peaks
27025 (qval < 1E-05)

hg38

Number of total reads
34448754
Reads aligned (%)
90.8
Duplicates removed (%)
5.6
Number of peaks
27140 (qval < 1E-05)

Base call quality data from DBCLS SRA