Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
STAG1

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
Human Mammary Epithelial Cells
cell line
MCF10A
cell type
Transformed nontumorigenic
experiment
ChIP-SEQ
chip antibody
custom made antibody for SA1 (STAG1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
IP step of the experiment was performed adding 20% of mouse chromatin to human chromatin (600ug)- 720ug in total per replicate. 72Ug of antibody was used per replicate. Samples went through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Adapter-ligated library was completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Median fragment size is 360 bp from which 120 bp correspond to adaptor sequences. Library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
31160777
Reads aligned (%)
70.9
Duplicates removed (%)
8.3
Number of peaks
2388 (qval < 1E-05)

hg38

Number of total reads
31160777
Reads aligned (%)
72.2
Duplicates removed (%)
7.3
Number of peaks
2462 (qval < 1E-05)

Base call quality data from DBCLS SRA