Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Lung
Cell type
Bronchial epithelial cells
NA
NA

Attributes by original data submitter

Sample

source_name
Bronchial epithelial cells
cell type
Bronchial epithelial cells
status
Healthy
Sex
mixed
passage
2
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
BECs were treated with hypotonic solution and mild detergent followed by clarification through sucrose gradient to isolate nuclei. Nuclei were treated with micrococcal nuclease (10U) for 10 minutes at 37°C, re pelleted and supernant containing mononucleosomes stored at 4°C. Mononuclesomal fractions were incubated with 4μg of H3K27ac antibody (Abcam, Ab4729) and 25μL Protein G dynabeads (Life Technologies) in modified RIPA buffer over night at 4°C. Bound complexes were washed and eluted and ChIP DNA extracted using phenol:chloroform/ethanol precipitation. Libraries were prepared using half total volume of eluted ChIP DNA and NEBNext® DNA Library Prep Master Mix Set and Multiplex Oligos for Illumina® (New England Biolabs). Library quality was assessed using Bioanalyzer 2100 High Sensitivity DNA Gels (Agilent).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
18776851
Reads aligned (%)
98.4
Duplicates removed (%)
2.4
Number of peaks
103 (qval < 1E-05)

hg19

Number of total reads
18776851
Reads aligned (%)
97.7
Duplicates removed (%)
2.6
Number of peaks
66 (qval < 1E-05)

Base call quality data from DBCLS SRA