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
breast cancer
cell line
MCF7

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, some samples were fixed for 10 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Chromatin DNA was sheared to 200–500 bp average in size by sonication. Soluble sheared chromatin was immunoprecipitated with specific antibodies or streptavidin beads overnight at 4°C. After washing and elution, the protein–DNA complex was decross-linked by heating at 65°C overnight. Immunoprecipitated DNA was purified by using iPure Diagenode kit. the libraries were constructed following Illumina's Chip-Seq Sample prep kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
58943607
Reads aligned (%)
95.5
Duplicates removed (%)
4.8
Number of peaks
1309 (qval < 1E-05)

hg19

Number of total reads
58943607
Reads aligned (%)
94.8
Duplicates removed (%)
6.3
Number of peaks
1381 (qval < 1E-05)

Base call quality data from DBCLS SRA