Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
cell line
cell line
MCF-7
ligand
Vehicle
time
45min

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed by incubation in 11% formaldehyde solution for 15 minutes at room temperature. Fixation was stopped by the addition of a 2.5 M glycine solution. Cells were washed in a 0.5% Igepal-PBS solution prior to snap-freezing. Active Motif (Carlsbad, CA) performed chromatin isolation, immunoprecipitation reactions, library generation and sequencing. ER ChIP reactions were conducted using 30 μg MCF7 breast cancer cell line chromatin and 4 μg of ER alpha antibody (sc-543, Santa Cruz Biotechnology, Dallas, TX). The ChIP reactions also contained a drosophila chromatin spike in for the normalization of the sequencing data. Libraries were prepared from each ER ChIP reaction, as well as an input/control DNA sample, and single-end sequencing data were generated on the Illumina platform

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
42087841
Reads aligned (%)
93.3
Duplicates removed (%)
39.0
Number of peaks
4521 (qval < 1E-05)

hg19

Number of total reads
42087841
Reads aligned (%)
92.7
Duplicates removed (%)
40.4
Number of peaks
4432 (qval < 1E-05)

Base call quality data from DBCLS SRA