Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RBPJ

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, RBPJ ChIP-seq
cell line
MDA-MB-231
chip antibody
RBPSUH(D10A4) (Cell Signaling, Catalog# 5313s, lot# 3)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody. Multiplexed ChIP-seq libraries were prepared at University of Michigan DNA Sequencing Core. 50-cycle single-end sequencing runs were performed on Illumina HiSeq 2500 at a sequencing depth of 30-40 million aligned reads per sample. Sequenced reads were preprocessed to trim adaptor sequences (Trimmomatic) and then aligned to human reference genome (hg19) using BWA software (version 0.7.15). 

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
103124853
Reads aligned (%)
82.8
Duplicates removed (%)
15.5
Number of peaks
2458 (qval < 1E-05)

hg38

Number of total reads
103124853
Reads aligned (%)
85.0
Duplicates removed (%)
13.9
Number of peaks
2952 (qval < 1E-05)

Base call quality data from DBCLS SRA