Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD9

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDAMB231 breast carcinoma cell line
cell line
MDAMB231
treatment
100nMJQ1 48h
culture media
DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone
library preparation kit
KAPA Hyper Prep
chip antibody
BRD9 Bethyl Laboratories A303-781A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies. All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
42095393
Reads aligned (%)
87.9
Duplicates removed (%)
6.3
Number of peaks
9841 (qval < 1E-05)

hg38

Number of total reads
42095393
Reads aligned (%)
90.7
Duplicates removed (%)
4.4
Number of peaks
9578 (qval < 1E-05)

Base call quality data from DBCLS SRA