Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM5B

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 line
MCF7
cell type
breast cancer cells
chip antibody
JARID1B (Novus Biologicals, 22260002)
transfection
siCTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Covaris focused-ultrasonicator. Following ChIP performed with specific antibodies and Dynabeads® Protein G (Invitrogen) ChIP DNA was subjected to end repair, A-tailing, ligation of Illumia single end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
155615959
Reads aligned (%)
40.9
Duplicates removed (%)
43.4
Number of peaks
47787 (qval < 1E-05)

hg38

Number of total reads
155615959
Reads aligned (%)
41.9
Duplicates removed (%)
42.3
Number of peaks
46969 (qval < 1E-05)

Base call quality data from DBCLS SRA