Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Muscle
Cell type
RH-4
NA
NA

Attributes by original data submitter

Sample

source_name
RH4
antibody
BRD4, Bethyl Lab (A301-985A100)
enrichment target
BRD4
condition
Epigenetic regulator
shRNA/target function
shRNA-scramble

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit). ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen). DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol. Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
26188819
Reads aligned (%)
82.2
Duplicates removed (%)
13.5
Number of peaks
6446 (qval < 1E-05)

hg38

Number of total reads
26188819
Reads aligned (%)
85.2
Duplicates removed (%)
11.1
Number of peaks
6371 (qval < 1E-05)

Base call quality data from DBCLS SRA