Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NRF1

Cell type

Cell type Class
Breast
Cell type
HCC1954
Primary Tissue
Breast
Site of Extraction
Soft Tissue
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
breast cancer cells
cell line
HCC1954
genotype
WT
chip antibody
NRF1 (Abcam, ab55744)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was carried out essentially as previously described (Jermann et al. PNAS 2014). Library Construction Protocol: Libraries for ChIP-seq were prepared according to standard Illumina library preparation protocols. Twelve cycles of PCR (NEB Q5 Hot Start HiFi PCR) were performed on end-repaired, A-tailed and adapter-ligated DNA prior to gel size-selection. Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
41562818
Reads aligned (%)
51.8
Duplicates removed (%)
37.2
Number of peaks
18318 (qval < 1E-05)

hg38

Number of total reads
41562818
Reads aligned (%)
53.2
Duplicates removed (%)
35.8
Number of peaks
18149 (qval < 1E-05)

Base call quality data from DBCLS SRA