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
siControl

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
109364729
Reads aligned (%)
66.1
Duplicates removed (%)
24.9
Number of peaks
42222 (qval < 1E-05)

hg38

Number of total reads
109364729
Reads aligned (%)
68.0
Duplicates removed (%)
23.3
Number of peaks
42656 (qval < 1E-05)

Base call quality data from DBCLS SRA