Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EHF

Cell type

Cell type Class
Lung
Cell type
NHBE
Tissue
epithelium
Lineage
endoderm
Description
bronchial epithelial cells

Attributes by original data submitter

Sample

source_name
EHF ChIP-seq
cell line
HBE cells
cell type
Primary human bronchial epithelial cells
chip antibody
EHF (Clone 5A.5)
input used for homer peak calling
HBE input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in lysis buffer (5mM PIPEs pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclear preparation was isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibody. DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. DNA was then incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPusreXP beads. Sequencing was performed on an Illumina Hi-Seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
56569934
Reads aligned (%)
50.6
Duplicates removed (%)
22.0
Number of peaks
5320 (qval < 1E-05)

hg38

Number of total reads
56569934
Reads aligned (%)
51.9
Duplicates removed (%)
20.5
Number of peaks
6130 (qval < 1E-05)

Base call quality data from DBCLS SRA