Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Breast
Cell type
LY2
NA
NA

Attributes by original data submitter

Sample

ENA first public
2014-10-21
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2177955
INSDC center alias
CRUK
INSDC center name
CRUK
INSDC first public
2014-10-21T17:04:38Z
INSDC last update
2018-03-08T16:43:10Z
INSDC status
public
Submitter Id
E-MTAB-1865:LY2
broker name
ArrayExpress
cell line
LY2
cell type
epithelial cell
common name
human
sample name
E-MTAB-1865:LY2
sex
female
specimen with known storage state
frozen specimen

Sequenced DNA Library

library_name
jc383
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF-7 cells [American Type Culture Collection (ATCC)] were grown in DMEM with 2mM L-glutamine, 10% fetal bovine serum, 50U/ml penicillin and 50ug/ml streptomycin in 37C incubator with 5% CO2. LY2 cells (kind gift from R. Clarke, Georgetown, Washington D.C.) were grown in phenol red-free MEM with 2mM L-glutamine, 10% charcoal dextrin stripped fetal bovine serum, 50U/ml penicillin and 50ug/ml streptomycin in 37C incubator with 5% CO2. Cells were steroid depleted for 3 days prior to treatment with Tamoxifen for 45 minutes. Proteins were cross linked to DNA by treating with formaldehyde (1%) for 10 minutes (ER) or 60 minutes (HMGB2). Chromatin immunoprecipitation and preparation of libraries was carried out as described in Schmidt et al (2009) Methods 48:240-248.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
26516872
Reads aligned (%)
99.2
Duplicates removed (%)
23.3
Number of peaks
65369 (qval < 1E-05)

hg19

Number of total reads
26516872
Reads aligned (%)
98.8
Duplicates removed (%)
23.9
Number of peaks
65345 (qval < 1E-05)

Base call quality data from DBCLS SRA