Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
BLaER2
NA
NA

Attributes by original data submitter

Sample

source_name
stem-like breast cancer cells
cell line
BPLER2
cell type
a stem-like breast cancer (BrCa) cell model
transforming gene
TERT; SV40-LT/st; HRASV12
treatment
DMSO
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates from formaldehyde cross-linked cells were clarified from sonicated nuclei and histone-DNA complexes were immunoprecipitated with antibody. Cross-links were reversed and DNA extracted for library construction. Libraries for paired-end sequencing and alignment were prepared according to NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® according to manufacturer instructions (New England BioLabs).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
25570097
Reads aligned (%)
96.5
Duplicates removed (%)
8.3
Number of peaks
816 (qval < 1E-05)

hg19

Number of total reads
25570097
Reads aligned (%)
95.5
Duplicates removed (%)
8.6
Number of peaks
578 (qval < 1E-05)

Base call quality data from DBCLS SRA