Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

ENA first public
2010-12-16
ENA last update
2018-03-08
External Id
SAMEA740759
INSDC center alias
CRUK-CRI
INSDC center name
CRUK-CRI
INSDC first public
2010-12-16T16:25:34Z
INSDC last update
2018-03-08T15:25:15Z
INSDC status
public
Submitter Id
E-MTAB-223:TAMr_ER_ChIP_veh
broker name
ArrayExpress
cell line
TAM_R
common name
human
disease state
breast cancer
sample name
E-MTAB-223:TAMr_ER_ChIP_veh
sex
female

Sequenced DNA Library

library_name
jc179_ER_ChIP_TAMR_45V_rep1_CRI01.fq
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RPMI 1640 medium por DMEM supplemented with 10% inactivated FBS, l-glutamine and PEST at 37C with 5% CO2. Antibodies were from Santa Cruz Biotechnology (sc-543), abcam (ab5089 and ab23738) and Millipore (07-729) and ChIP was performed using 10e7-10e8 cells per reaction. Briefly, crosslinking of protein and DNA was done in room temperature for 10 minutes with serum free media containing 0,37 % formaldehyde. Cells were scraped and washed in PBS before treatment of cell lysis buffer with protease inhibitors on ice. Pelleted nuclei were resuspeded in RIPA buffer and a BioRuptor (Diagenode) was used to sonicate DNA. ChIP was performed with 10 micrograms of antibody. ChIP DNA was gel fractionated and amplified to create two size libraries corresponding to insert sizes of 200-300 bp. For DNase I hypersensitivity was performed as previously described (Eeckhoute et al., 2006). Digested DNA was run on a gel and the digested material (between 200bp and 500bp in size). For all ChIPs washing was done six times with RIPA buffer and once with TE-buffer and DNA-protein complexes were eluted from beads twice with 200 microlitres of 0.1 M NaHCO3 and 1 % SDS and treated with RNAseA at 65C for 6 hours and Proteinase K at 45C over night. Chromatin was amplified with Solexa protocol chromatin amplification.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
15043403
Reads aligned (%)
49.5
Duplicates removed (%)
48.8
Number of peaks
1527 (qval < 1E-05)

hg38

Number of total reads
15043403
Reads aligned (%)
51.9
Duplicates removed (%)
46.9
Number of peaks
1459 (qval < 1E-05)

Base call quality data from DBCLS SRA