Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Lung
Cell type
IMR-90
Primary Tissue
Lung
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
IMR90 human fibrobasts
cell line
IMR90
cell type
fibrobasts
antibody
Brd4 (A301-985A; Bethyl)
treatment
senescent

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Five to 30 million IMR90 cells were crosslinked for 10 minutes using 1 % formaldehyde, followed by quenching with 0.125M glycine for 10 minutes. To prepare chromatin from crosslinked-senescent cells, aliquots of less than 1 million cells were kept in individual eppendorf tubes for sonication to maximize the chromatin fragmentation efficiency. After purifying immunoprecipitated DNA, a TruSeq ChIP Sample Prep Kit (Illumina) was used to construct the ChIP-Seq library following the manufacturer's protocol except for amplifying the adaptor-ligated library for 15 cycles. ChIP-Seq libraries were sequenced using an illumina HiSeq 2000 platform with single end reads of 50 bases. Four libraries at equal molarity were pooled to aim for a sequencing depth of 20-40 million aligned reads per sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
107334951
Reads aligned (%)
22.8
Duplicates removed (%)
73.8
Number of peaks
2231 (qval < 1E-05)

hg38

Number of total reads
107334951
Reads aligned (%)
25.0
Duplicates removed (%)
71.4
Number of peaks
2479 (qval < 1E-05)

Base call quality data from DBCLS SRA