Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me3

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

age
69 year
dev stage
adult
donor ID
ENCDO000AAE
sex
female
health state
breast cancer (adenocarcinoma)
sample type
immortalized cell line
cell line
MCF-7
passage number
146
lab
Bradley Bernstein, Broad

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
extraction method: see document general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
89754181
Reads aligned (%)
93.9
Duplicates removed (%)
11.2
Number of peaks
5131 (qval < 1E-05)

hg19

Number of total reads
89754181
Reads aligned (%)
92.0
Duplicates removed (%)
15.7
Number of peaks
2454 (qval < 1E-05)

Base call quality data from DBCLS SRA