Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

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
MCF7L parental
cell types
immortalized breast epithelial cell line
chip antibody
H3K4me3
agent
treated with E2
time point
24 hours

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA extracted using Quick-RNA MiniPrep Kit from ZYMO Research TCC was performed as described (Kalhor et al. 2012). ChIP-seq and RNA-seq libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
57936955
Reads aligned (%)
97.7
Duplicates removed (%)
10.8
Number of peaks
24744 (qval < 1E-05)

hg19

Number of total reads
57936955
Reads aligned (%)
96.8
Duplicates removed (%)
12.3
Number of peaks
24262 (qval < 1E-05)

Base call quality data from DBCLS SRA