Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ESR1

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
Human breast cancer cell line
condition
Tam-Responsive
tissue
MCF7
antibody
anti-ER (SC-543, Santa Cruz Biotechnologies)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP in the tumours and metastases, the frozen sample was cut into smaller pieces and thawed in 1% (final concentration) formaldehyde for 20 minutes at room temperature. The reaction was quenched by adding 0.1 volume of 2M glycine for 10 minutes. The sample was disaggregated by Dounce homogenisation and processed according to standard ChIP procedures (Schmidt D et al, Methods, doi:S1046-2023(09)00047-4 [pii]). The DNA was subsequently amplified as previously described (Schmidt D et al, Methods, doi:S1046-2023(09)00047-4 [pii]). For the malignantpericardial effusion, epithelial cells were first enriched using Dynabeads conjugated with Epcam. For ChIPs from cell line material, proliferating cells were cross-linked and processed for ChIP as previously described (Schmidt D et al, Methods, doi:S1046-2023(09)00047-4 [pii]). For the TAM-R cells, ER ChIP-seq was performed on cells grown in DMEM containing 10% FBS and 10 nM tamoxifen for 24 hours. For the cocktail experiments, cells weretreated with 100 ng/ml IGF-1, 100 ng/ml EGF, 1 ng/ml TNF-alpha and 10 ng/ml IL-6 for 90 minutes.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
22274527
Reads aligned (%)
75.7
Duplicates removed (%)
24.0
Number of peaks
48646 (qval < 1E-05)

hg38

Number of total reads
22274527
Reads aligned (%)
75.9
Duplicates removed (%)
23.9
Number of peaks
48667 (qval < 1E-05)

Base call quality data from DBCLS SRA