Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Blood
Cell type
Lymphoblastoid cell line
Tissue
blood
Lineage
mesoderm
Description
parental cell type to lymphoblastoid cell lines

Attributes by original data submitter

Sample

source_name
GM15850 LCLs (FRDA)
antibody
BRD4
cell line
GM15850 LCLs (FRDA)
treatment
1000nM Syn-TEF1
treatment time
24 h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were chemically crosslinked by the addition of 4 mL of 1.5% formaldehyde in PBS per 10 cm2 dish for 15 min at room temperature. Cells were resusupended in Lysis Buffer 1 (50 mM HEPES , pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL, 0.25% Triton X-100, 1X HALT protease inhibitor) and 3T3 mouse embryonic fibroblast cells (formaldehyde fixed as above) equivalent to 10% GM15850 cells were added to each sample for downstream ChIP-RX analysis. NGS libraries were generated with Thruplex DNAseq Single Index Kit (Rubicon) and sequenced (single end, 150 bp reads) via NextSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
47645257
Reads aligned (%)
67.3
Duplicates removed (%)
10.6
Number of peaks
28442 (qval < 1E-05)

hg38

Number of total reads
47645257
Reads aligned (%)
68.3
Duplicates removed (%)
10.5
Number of peaks
28020 (qval < 1E-05)

Base call quality data from DBCLS SRA