Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD1

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDA-MB-231
cell type
Breast cancer derived cell line
cell line
MDA-MB-231
treatment
Untreated
antibody
pSMAD1/5, Cell Signaling Technologies 11971

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cross-linking with 4% formaldehyde for 5 min at room temperature followed by isolation of nuclei, sonication and immunoprecipitation. Following end repair, poly-A-tailing and adapter ligation, Illumina TruSeq ChIP sample preparation kits were used to generate the libraries. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems, Cape Town, South Africa). The PCR was run before gel isolation using the Invitrogen SizeSelect E-gel system (SizeSelect gel protocol, Thermo Fisher Scientific). Post PCR we used AMPure XP beads (AMPure bead protocol, Beckman Coulter, Inc.) at a 1:1 ratio to maintain size integrity. Samples were multiplexed and 101-bp single end reads were generated on an Illumina HiSeq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
58118954
Reads aligned (%)
58.2
Duplicates removed (%)
35.2
Number of peaks
1002 (qval < 1E-05)

hg38

Number of total reads
58118954
Reads aligned (%)
60.2
Duplicates removed (%)
33.5
Number of peaks
1659 (qval < 1E-05)

Base call quality data from DBCLS SRA