Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD3

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
SMAD3 (Abcam, ab28379)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After sonication, clarified nuclear lysates were pre-cleared with Protein A/G agarose for 1 hour. Pre-cleared lysates were then immunoprecipitated with 10 μg SMAD3 antibody (ab28379) overnight at 4°C. Protein A/G agarose blocked with BSA were added for 2 hours the next day, and beads were washed extensively. 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

hg19

Number of total reads
64207378
Reads aligned (%)
63.7
Duplicates removed (%)
35.5
Number of peaks
20172 (qval < 1E-05)

hg38

Number of total reads
64207378
Reads aligned (%)
64.4
Duplicates removed (%)
35.0
Number of peaks
20291 (qval < 1E-05)

Base call quality data from DBCLS SRA