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
MCF-7 cells
cell line
MCF-7

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum. Approximately 5 x 107 cells were used for each ChIP-seq assay. The chromatin DNA precipitated by polyclonal antibodies against UTX. The DNA was purified with the Qiagen PCR purification kit. The 1st strand cDNA was synthesized with random primer flanked by 7 nt sequence to track infromation. The 2nd strand DNA was generated with N6 adaptor. The resulting DNA libraries were amplified with Phusion High-Fidelity DNA Polymerase.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
20806208
Reads aligned (%)
91.1
Duplicates removed (%)
16.4
Number of peaks
725 (qval < 1E-05)

hg19

Number of total reads
20806208
Reads aligned (%)
90.3
Duplicates removed (%)
16.7
Number of peaks
284 (qval < 1E-05)

Base call quality data from DBCLS SRA