Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM5B

Cell type

Cell type Class
Breast
Cell type
SUM 185PE
Primary Tissue
Unknown
Tissue Diagnosis
Anaplastic Carcinoma

Attributes by original data submitter

Sample

source_name
breast cancer cells
cell line
SUM185PE
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
183521370
Reads aligned (%)
31.9
Duplicates removed (%)
59.2
Number of peaks
52940 (qval < 1E-05)

hg38

Number of total reads
183521370
Reads aligned (%)
32.9
Duplicates removed (%)
58.1
Number of peaks
51998 (qval < 1E-05)

Base call quality data from DBCLS SRA