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 cells
cell types
Human-derived breast cancer cells
tissue
mammary gland
cell line
MCF7
protocol
glucose free medium
antibody
CTCF antibody
antibody vendor
Cell Signaling Technology
antibody catalogy no
#3418S

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with CTCF antibody (Cell Signaling Technology, Cat: #3418S). ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
41774596
Reads aligned (%)
59.0
Duplicates removed (%)
37.6
Number of peaks
58279 (qval < 1E-05)

hg38

Number of total reads
41774596
Reads aligned (%)
59.3
Duplicates removed (%)
37.5
Number of peaks
58517 (qval < 1E-05)

Base call quality data from DBCLS SRA