Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
MCF10Asi-ER cells
cell line
MCF10A
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody. ChIP-seq libraries were prepared from 10 ng of ChIP (or Input) DNA with TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer’s instructions. 50bp single-end sequencing was performed using Illumina HiSeq 2000 platform (Genomix4life S.R.L., Baronissi, Salerno, Italy) according to standard operating procedures.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
21931464
Reads aligned (%)
90.4
Duplicates removed (%)
4.1
Number of peaks
1035 (qval < 1E-05)

hg19

Number of total reads
21931464
Reads aligned (%)
89.3
Duplicates removed (%)
5.4
Number of peaks
1054 (qval < 1E-05)

Base call quality data from DBCLS SRA