Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7L parental
cell types
immortalized breast epithelial cell line
chip antibody
CTCF
agent
treated with E2
time point
1 hour

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA extracted using Quick-RNA MiniPrep Kit from ZYMO Research TCC was performed as described (Kalhor et al. 2012). ChIP-seq and RNA-seq libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
113941161
Reads aligned (%)
78.7
Duplicates removed (%)
19.7
Number of peaks
67683 (qval < 1E-05)

hg38

Number of total reads
113941161
Reads aligned (%)
80.9
Duplicates removed (%)
18.1
Number of peaks
68704 (qval < 1E-05)

Base call quality data from DBCLS SRA