Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED1

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
MCF7-E2-CHIP-MED1
cell line
MCF7 (ATCC, HTB-22)
cell type
Breast adenocarcinoma-derived cells
passages
N/A
treated with
100nM E2, 120min
chip antibody
MED1 (Bethyl, A300-793A, lot:2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde in culture medium for 10 minutes at room temperature. Cells were then lysed in 10 ml lysis buffer (0.1%SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl ph 8.0 and 150 mM NaCl) and chromatin was sheared to 200-600 bp fragments using a Bioruptor Sonicator (Diagenode). Chromatin extract from 5x10^7 cells was incubated overnight at 4oC with 100 ul of Dynabeads Protein G magnetic beads (Life Technologies, 10004D) previously incubated with 10 ug of selected antibodies. After ChIP, samples were washed and bound complex were reversed cross-linked and eluted in 10mM Tris-HCl pH 8 The TruSeq DNA sample prep kit with indexing adapters was used according to the manufacturer's recommendations (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
16763509
Reads aligned (%)
90.8
Duplicates removed (%)
2.7
Number of peaks
1031 (qval < 1E-05)

hg38

Number of total reads
16763509
Reads aligned (%)
92.5
Duplicates removed (%)
1.7
Number of peaks
963 (qval < 1E-05)

Base call quality data from DBCLS SRA