Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PCGF2

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
cell line
MDA-MB-231
cell type
Mammary gland adenocarcarcinoma epithelial cells derived from metastatic site
cell source
ATCC #HTB-26
modifications
Parental cells
chip antibody
Santa Cruz # sc-10744 X

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were grown to 80% confluence on 150cm plates and processed using the High Sensitivity ChIP-IT Kit (Active Motif cat #53040). Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
100550347
Reads aligned (%)
25.3
Duplicates removed (%)
72.9
Number of peaks
2543 (qval < 1E-05)

hg38

Number of total reads
100550347
Reads aligned (%)
31.6
Duplicates removed (%)
66.8
Number of peaks
6262 (qval < 1E-05)

Base call quality data from DBCLS SRA