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
MCF7
cell line
MCF7
treatment
Ethanol as vehicle control
antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immuoprecipitation (ChIP) experiments with MCF7 cells were performed as previously described (Tsai et al, Nature, 2010. PMID:21164480). Briefly, the fragmented chromatin lysate was immunoprecipitated overnight using TRIM24 antibody. The protein-DNA complexes were washed several times and the phenol-chloroform-extracted DNA was used for library construction and sequencing. For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg38

Number of total reads
170560981
Reads aligned (%)
94.8
Duplicates removed (%)
8.1
Number of peaks
120096 (qval < 1E-05)

hg19

Number of total reads
170560981
Reads aligned (%)
94.1
Duplicates removed (%)
10.0
Number of peaks
136173 (qval < 1E-05)

Base call quality data from DBCLS SRA