Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

Cell type

Cell type Class
Breast
Cell type
HMEC
Primary Tissue
Breast
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Human Mammary Epithelial Cells (HMEC)
cell type
Primary cells
experiment
ChIP-SEQ
catalogue number
Lonza CC-2551
passages
less than 10
chip antibody
custom made antibody for SMC1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
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
Illumina HiSeq 2000

hg19

Number of total reads
99790629
Reads aligned (%)
80.6
Duplicates removed (%)
7.7
Number of peaks
50756 (qval < 1E-05)

hg38

Number of total reads
99790629
Reads aligned (%)
81.9
Duplicates removed (%)
6.7
Number of peaks
51310 (qval < 1E-05)

Base call quality data from DBCLS SRA