Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Breast
Cell type
MCF 10A
Primary Tissue
Breast
Tissue Diagnosis
Fibrocystic Disease

Attributes by original data submitter

Sample

source_name
Breast epithelial cell line, MCF10A MII
cell line
MCF10A MII
cell type
Breast epithelial cell line
transformation
H-Ras transformed
treatment
TGFβ3, 5 ng/ml, 16h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin isolation, sonication and immunoprecipitation using anti-SMAD2/3 antibody (#610843, BD Transduction Laboratories) were performed essentially as described (Isogaya et al., 2014; Morikawa et al., 2016). The library was prepared using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England Biolabs) or KAPA DNA Library Preparation Kits for Illumina (KAPA Biosystems).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
39823765
Reads aligned (%)
89.7
Duplicates removed (%)
36.5
Number of peaks
1161 (qval < 1E-05)

hg19

Number of total reads
39823765
Reads aligned (%)
89.0
Duplicates removed (%)
38.0
Number of peaks
1142 (qval < 1E-05)

Base call quality data from DBCLS SRA