Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TRIM24

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 E2neg
cell line
MCF7
treatment
Ethanol as vehicle control
antibody
TRIM24 (Novus Biologicals)

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

hg19

Number of total reads
44286540
Reads aligned (%)
89.9
Duplicates removed (%)
3.4
Number of peaks
1195 (qval < 1E-05)

hg38

Number of total reads
44286540
Reads aligned (%)
91.7
Duplicates removed (%)
2.1
Number of peaks
381 (qval < 1E-05)

Base call quality data from DBCLS SRA