Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
T-47D
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
Breast Cancer Cell
cell line
T47D
passages
5 to 10
chip-antibody
Non applicable

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell samples were crosslinked with 1% formaldehyde for 10 min, and quenched by glycine to a 125nM final concentration. The fixed cells were lysed in SDS buffer and the chromatin was sheared by Covaris sonication. The sheared chromatin was incubated with the indicated antibodies and protein G-Dynabeads. The samples underwent decrosslinking, RNase and proteinase K treatment. DNA fragments were eluted using AMP Pure beads, library was prepared and samples were subjected to high-throughput sequencing using HiSeq 2000 platform (Illumina). ChIP-seq libraries were prepared using 10 ng of DNA and Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
25082707
Reads aligned (%)
99.0
Duplicates removed (%)
4.1
Number of peaks
825 (qval < 1E-05)

hg19

Number of total reads
25082707
Reads aligned (%)
98.0
Duplicates removed (%)
5.3
Number of peaks
926 (qval < 1E-05)

Base call quality data from DBCLS SRA