Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
Human breast cells
cell type
MCF7
antibody vendor
Millipore

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Performed with Illumina protocol. 10Ng of inmunoprecipitated DNA was en-repaired, and Illumina double stranded adapters for single read sequencing were ligated to the DNA. After purification of the sample with a MinElute spin column, we size the selected libraries on a 2% agarose gel and fragments corresponding to an insert size range of around 130bp were recovered. The libraries were finally amplified with an 18-cycle PCR reaction, and library quality was confirmed on the Agilent 2100 Bioanalyzer. The samples were loaded at concentrations of 8-11 pm onto Illumina single read flowcells and sequenced on the Illumina Genome Analyzer Iix using a 40 cycles recipe.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
10911458
Reads aligned (%)
59.9
Duplicates removed (%)
28.9
Number of peaks
99 (qval < 1E-05)

hg19

Number of total reads
10911458
Reads aligned (%)
59.1
Duplicates removed (%)
29.4
Number of peaks
59 (qval < 1E-05)

Base call quality data from DBCLS SRA