Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CBX5

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
chip antibody
HP1_alpha
antibody vendor
Abcam

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

hg19

Number of total reads
10697452
Reads aligned (%)
84.1
Duplicates removed (%)
31.9
Number of peaks
1174 (qval < 1E-05)

hg38

Number of total reads
10697452
Reads aligned (%)
85.5
Duplicates removed (%)
30.7
Number of peaks
1230 (qval < 1E-05)

Base call quality data from DBCLS SRA