Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7 Breast cancer
cell line
MCF-7
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq libraries were prepared from 10ng fragmented DNA using the NEBNext ChIP-Seq Library Prep Master Mix Kit (NEB-E6240S). Accordingly, after end-repair and A-tailing sequencing, adaptors were ligated and size selection of adaptor-ligated DNA using AMPure XP Beads (Beckman Coulter) performed. Libraries were enriched with 12 PCR cycles and sequenced according to manufacturer’s protocol on an Illumina HiSeq2000 instrument

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
202235039
Reads aligned (%)
99.5
Duplicates removed (%)
17.5
Number of peaks
2953 (qval < 1E-05)

hg19

Number of total reads
202235039
Reads aligned (%)
98.5
Duplicates removed (%)
18.1
Number of peaks
984 (qval < 1E-05)

Base call quality data from DBCLS SRA