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 cells
chip-antibody
Input
cell type
Luminal cells
cell line
T47D

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. ChIPseq libraries were prepared by following Rubicon Thruplex-FD kit. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by PAGE gel electrophoresis and purified.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
46683393
Reads aligned (%)
88.7
Duplicates removed (%)
4.3
Number of peaks
1487 (qval < 1E-05)

hg19

Number of total reads
46683393
Reads aligned (%)
87.7
Duplicates removed (%)
5.8
Number of peaks
987 (qval < 1E-05)

Base call quality data from DBCLS SRA