Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Epitope tags

Cell type

Cell type Class
Breast
Cell type
WHIM12
NA
NA

Attributes by original data submitter

Sample

source_name
Human triple-negative breast cancer cells
cell line
WHIM12
cell type
triple-negative breast cancer
chip antibody
V5 (Abcam, ab9116)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 15 min at 37°C. Crosslinking was quenched with 0.125 M glycine for 5 min at 4°C, followed by multiple washes with cold PBS. Nuclei were harvested via hypotonic lysis and subjected to sonication in a lysis buffer containing 1% SDS. Sheared chromatin lysates were then pre-cleared with Protein A/G agarose beads for 1 hour, followed by immunoprecipitation with appropriate antibody overnight at 4°C. Protein A/G agarose beads blocked with BSA were added to lysates for 2 hours the next day, followed by extensive washes. Protein/DNA complexes were eluted from the beads with 100 mM NaHCO3 and 1% SDS, and de-crosslinking was carried out overnight at 65°C. RNA and protein were digested with RNase A and Proteinase K, respectively. DNA was purified using phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated overnight at -20°C. Libraries of ChIP DNA were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems) according to manufacturer's instructions, and samples were multiplexed with Illumina adapters (NEB).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
73488739
Reads aligned (%)
99.0
Duplicates removed (%)
17.0
Number of peaks
2231 (qval < 1E-05)

hg19

Number of total reads
73488739
Reads aligned (%)
98.5
Duplicates removed (%)
18.4
Number of peaks
1708 (qval < 1E-05)

Base call quality data from DBCLS SRA