Antigen

Antigen Class

TFs and others

Antigen

BRD4

Cell type

Cell type Class

Breast

Cell type

SUM 149PT

Primary Tissue

Breast

Tissue Diagnosis

Adenocarcinoma Ductal

Sample

source_name

SUM149

cell line

SUM149

chip antibody

BRD4 (Bethyl, catalog# A301-985A, lot# 4)

drug treatment

JQ1

duration

12 hour

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

69085410

Reads aligned (%)

97.2

Duplicates removed (%)

65.3

Number of peaks

2946 (qval < 1E-05)

hg19

Number of total reads

69085410

Reads aligned (%)

96.2

Duplicates removed (%)

69.3

Number of peaks

1398 (qval < 1E-05)