Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

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

ENA first public
2019-02-08
ENA last update
2018-06-11
ENA-CHECKLIST
ERC000011
External Id
SAMEA4722178
INSDC center alias
Laboratory of Molecular Medicine and Genomics
INSDC center name
Laboratory of Molecular Medicine and Genomics
INSDC first public
2019-02-08T17:04:05Z
INSDC last update
2018-06-11T13:57:32Z
INSDC status
public
Submitter Id
E-MTAB-6883:Sample 18
broker name
ArrayExpress
cell line
MCF-7
cell type
mammary epithelial cell
common name
human
disease
invasive ductal carcinoma
metastatic site
pleural effusion
organism part
mammary gland
sample name
E-MTAB-6883:Sample 18

Sequenced DNA Library

library_name
Sample 18_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. None ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. ChIP-Seq experiments were performed in three biological replicates in MCF-7 cells, in exponential growing condition. Cells were treated with ICI 182,780 10-7 M for 3 days and with EPZ004777 6.4 µM or DMSO for 6 days. ChIP-Seq experiments were performed in three biological replicates in MCF-7 cells, in exponential growing condition. Cells were treated with ICI 182,780 10-7 M for 3 days and with EPZ004777 6.4 µM or DMSO for 6 days. We used antibodies to ERα (HC-20) (Santa Cruz Biotechnology, SC-8002), Dot1l Antibody (Bethyl Laboratories, A300-954A), and rabbit IgG antiobody as negative control. Cells lysis, sonication and binding were performed as described by Serandour AA et al, 2013. After binding, beads washing, elution, reverse crosslinking and DNA extraction were then performed as described in Ambrosino et al, 2010. 1µl aliquot of DNA obtained was analysed to asses size distribution by Agilent Genomic DNA ScreenTape & Reagents using an Agilent 4200 TapeStation System (Agilent Technologies). The concentration of each DNA sample was determined by using Quant-IT DNA Assay Kit-High Sensitivity and a Qubit Fluorometer (Life Technologies). 10 ng of each purified ChIP DNA were used for sequencing libraries preparation with TruSeq ChIP Sample Prep Kit (Illumina Inc.).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
47704662
Reads aligned (%)
97.9
Duplicates removed (%)
20.2
Number of peaks
1628 (qval < 1E-05)

hg19

Number of total reads
47704662
Reads aligned (%)
97.0
Duplicates removed (%)
22.3
Number of peaks
1306 (qval < 1E-05)

Base call quality data from DBCLS SRA