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
Human breast cancer cell line
cell line
MCF7+BORIS (Clone1, single-cell clone of MCF7 cell, stably expressing BORIS)
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
After overnight incubation with DiaMag magnetic beads (Diagenode, Inc.) and CTCF or BORIS monoclonal or polyclonal antibodies (characterized and described by PMID:15731119; PMID: 21659515; PMID:20231363), precipitated chromatin was then washed, decrosslinked, and digested with proteinase K. The resulting DNA was purified using phenol/chloroform/isoamyl alcohol. DNA concentration was assessed with Quant‐it PicoGreen dsDNA kit (Invitrogen) and 5–10 ng was used to generate sequencing libraries. 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
37999255
Reads aligned (%)
84.5
Duplicates removed (%)
11.1
Number of peaks
64849 (qval < 1E-05)

hg38

Number of total reads
37999255
Reads aligned (%)
86.6
Duplicates removed (%)
9.6
Number of peaks
66836 (qval < 1E-05)

Base call quality data from DBCLS SRA