Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SPDEF

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
cell type
MCF-7 breast cancer cell line
chip antibody
SPDEF (sc67022; Santa Cruz Biotechnology)
chip treatment conditions
Full media

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP of DNA was performed as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001 Illumina sequencing libraries were prepared as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
32416721
Reads aligned (%)
98.4
Duplicates removed (%)
32.3
Number of peaks
561 (qval < 1E-05)

hg19

Number of total reads
32416721
Reads aligned (%)
97.8
Duplicates removed (%)
33.4
Number of peaks
736 (qval < 1E-05)

Base call quality data from DBCLS SRA