Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

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
Primary human bronchial epithelial cells
cell type
HBE
antibody
H3K4me3 (Millipore 07-743)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNase-seq: genomic DNA was digested with different concentrations of DNaseI (NEB) and purified for library construction (Boyle et al. Cell, 2008). ChIP-seq: Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were 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 the histone antibodies. DNase-seq: libraries were prepared by Drs A. Safa and G. Crawford. ChIP-seq: DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then 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 AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
46471558
Reads aligned (%)
92.0
Duplicates removed (%)
15.0
Number of peaks
25578 (qval < 1E-05)

hg19

Number of total reads
46471558
Reads aligned (%)
91.3
Duplicates removed (%)
16.4
Number of peaks
26409 (qval < 1E-05)

Base call quality data from DBCLS SRA