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
2017-09-05
ENA last update
2017-04-05
ENA-CHECKLIST
ERC000011
External Id
SAMEA103957833
INSDC center alias
Laboratory of Molecular Medicine and Genomics Department of Medicine and Surgery University of Salerno
INSDC center name
Laboratory of Molecular Medicine and Genomics Department of Medicine and Surgery University of Salerno
INSDC first public
2017-09-05T17:02:08Z
INSDC last update
2017-04-05T12:52:44Z
INSDC status
public
Submitter Id
E-MTAB-4359_2:Sample 8
broker name
ArrayExpress
cell line
MCF-7
common name
human
disease
breast carcinoma
genotype
expression of estrogen receptor beta fused to C terminus tandem affinity purification tag
sample name
E-MTAB-4359_2:Sample 8

Sequenced DNA Library

library_name
Sample 8_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
C-TAP-ERβ and MCF7 control cells were hormone-deprived for 5 days For each assay, a total of 5 × 106 cells were fixed, lysed, sonicated and diluted as earlier described29. An aliquot of whole-cell extract was taken as input. For ERβ immunoprecipitation, chromatin samples were incubated at 4°C for 3 hours with 30µl of IgG Sepharose 6 fast Flow (GE Healthcare Bio-Science AB) properly equilibrated in a Poly-Prep chromatography columns (0.84 cm, Bio-Rad), according to the manufacturer’s instructions. For Ago2 immunoprecipitation, chromatin samples were incubated at 4°C overnight with 1µg of mouse monoclonal anti-Ago2/eIF2C2 (ab57113, Abcam) and then at 4°C for 1 hour with 40 µl of equilibrated slurry Protein A/G Plus-Agarose (sc-2003, Santa Cruz Biotechnology). As negative control of Ago2 immunoprecipitation, chromatin samples were also incubated overnight with 1 µg of mouse monoclonal anti-Flag M2 affinity purified (F1804, Sigma-Aldrich). Beads washing, elution, reverse crosslinking and DNA extraction were then performed as described29. Size distribution of each ChIP DNA sample was assessed by running a 1µl aliquot on Agilent High Sensitivity DNA chip using an Agilent Technologies 2100 Bioanalyzer (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 purified ChIP DNA were used as starting material for sequencing libraries preparation, by pooling three independent ChIP experiments. Indexed libraries were prepared with TruSeq ChIP Sample Prep Kit (Illumina Inc.).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
42158425
Reads aligned (%)
95.8
Duplicates removed (%)
21.1
Number of peaks
1155 (qval < 1E-05)

hg19

Number of total reads
42158425
Reads aligned (%)
95.0
Duplicates removed (%)
22.8
Number of peaks
1220 (qval < 1E-05)

Base call quality data from DBCLS SRA