Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Epitope tags

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
MDA-MB-231
genotype
wild type
cell line
MDA-MB-231
tumor type
Triple-negative breast cancer
chip antibody
HA antibody (Abcam, ab9110)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with HA antibody. Approximately 2-5 ng of ChIPed DNA from each condition was used to generate the ChIP-seq library using the Ovation Ultralow DR Multiplex System 1-8 Kit (NuGEN Technologies), according to the manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
119150413
Reads aligned (%)
97.2
Duplicates removed (%)
22.8
Number of peaks
1877 (qval < 1E-05)

hg19

Number of total reads
119150413
Reads aligned (%)
96.9
Duplicates removed (%)
23.3
Number of peaks
2189 (qval < 1E-05)

Base call quality data from DBCLS SRA