Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Breast
Cell type
T-47D
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
T47D-MTVL breast cancer cell line
treatment
unstimulated cells
chip antibody
anti-H3K4me3 (Upstate-millipore AB+,17-678)
cell type
T47D-MTVL breast cancer cell line

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After hormone treatment, the medium was replaced by medium containing 1% formaldehyde and incubated 10 min at 37ºC for cross-linking. The reaction was stop by adding 125 mM glycine and incubated 5 min at room temperature. Cells were washed twice with cold PBS, and collected. Preparation of chromatin and ChIP experiments were performed as previously described (Strutt et al, Methods Mol Biol. 1999; 119:455-567). Immunoprecipitated DNA was purified by phenol:chloroform followed by ethanol precipitation It was performed using the NEBNext DNA sample prep Reagents set 1

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
12248135
Reads aligned (%)
84.2
Duplicates removed (%)
7.3
Number of peaks
11371 (qval < 1E-05)

hg19

Number of total reads
12248135
Reads aligned (%)
83.5
Duplicates removed (%)
8.4
Number of peaks
11474 (qval < 1E-05)

Base call quality data from DBCLS SRA