A carrier-assisted ChIP-seq method for Estrogen Receptor-chromatin interactions from breast cancer core needle biopsy samples
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Breast
Cell type
Mammary epithelial cells
NA
NA
Attributes by original data submitter
Sample
ENA first public
2013-04-01
ENA last update
2018-03-08
External Id
SAMEA1713770
INSDC center alias
Cancer Research UK Cambridge Institute
INSDC center name
Cancer Research UK Cambridge Institute
INSDC first public
2013-04-01T17:02:48Z
INSDC last update
2018-03-08T16:18:13Z
INSDC status
public
Submitter Id
E-MTAB-1534:BIOPSY_3691
broker name
ArrayExpress
cell type
epithelial
common name
human
disease state
breast cancer
organism part
breast
sample name
E-MTAB-1534:BIOPSY_3691
sex
female
Sequenced DNA Library
library_name
jc710
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Tissue for ChIP-seq analyses was from patients who were treated at the Netherlands Cancer Institute.Three biopsies (14-gauge, 15 mm thick) were taken from each tumour, two of which where frozen with liquid nitrogen and one was formalin-fixed for direct clinical assessment. Tumour cell percentage was determined using Hematoxylin and Eosin (H&E), and tissue was only used for ChIP-seq analysis when tumour cell percentage was higher then 50%. All samples stained positive for Estrogen Receptor. Samples were processed and chromatin was extracted as described (Schmidt et al., Methods 48:3 pp240-248 2009) but with a number of modifications. During the immunoprecipitation, 100mg/ml glycogen (Invitrogen) or 20mg/ml recombinant histone 2B (M2505S; New England Biolabs) and 1mg/ml human mRNA (Invitrogen) was added as carriers for the ChIP. During the entire procedure, non-sticky eppendorf tubes were used (13-698-794; Fisher Scientific).