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
cell line
MCF7
cell type
Breast cancer cell line
shRNA
Control
treatment
Veh
chip antibody
MED1 (Santa Cruz, sc-74475 and Bethyl laboratories, A300-793A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody or by streptavidin magnet beads pull-down. The extracted ChIP DNA was ligated to specific adaptors of KAPA Hyper Prep system (KK8504), according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
24814669
Reads aligned (%)
78.1
Duplicates removed (%)
19.7
Number of peaks
879 (qval < 1E-05)

hg38

Number of total reads
24814669
Reads aligned (%)
80.0
Duplicates removed (%)
18.5
Number of peaks
756 (qval < 1E-05)

Base call quality data from DBCLS SRA