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
Breast Cancer Cell Line
cell line
MCF7
genotype
wild type (wt)
expressed vector
none
treatment
none
chip antibody
custom mouse monoclonal CTCF (characterized in PMID:15731119)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch). DNA concentration was assessed with a Qubit4 (ThermoFisher) and 5–10 ng was used to generate sequencing libraries using a TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
33765559
Reads aligned (%)
85.9
Duplicates removed (%)
12.5
Number of peaks
60256 (qval < 1E-05)

hg38

Number of total reads
33765559
Reads aligned (%)
88.1
Duplicates removed (%)
11.0
Number of peaks
61582 (qval < 1E-05)

Base call quality data from DBCLS SRA