Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD3

Cell type

Cell type Class
Breast
Cell type
SUM 159PT
Primary Tissue
Breast
Tissue Diagnosis
Anaplastic Carcinoma

Attributes by original data submitter

Sample

source_name
Human triple-negative breast cancer cells
cell line
SUM159
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
62395039
Reads aligned (%)
63.9
Duplicates removed (%)
35.2
Number of peaks
14562 (qval < 1E-05)

hg38

Number of total reads
62395039
Reads aligned (%)
64.5
Duplicates removed (%)
34.8
Number of peaks
14532 (qval < 1E-05)

Base call quality data from DBCLS SRA