Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NFE2L2

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
A549
cell type
Human lung adenocarcinoma epithelial A549 cells
cell line
A549
cell type
lung adenocarcinoma
genotype/variation
wildtype
chip antibody
anti-NRF2 (Santa Cruz, sc-13032, lot C1416)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein A (for Nrf2) or G (for Pol2) agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of target specific antibody. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenolchloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
38759327
Reads aligned (%)
51.6
Duplicates removed (%)
32.4
Number of peaks
4317 (qval < 1E-05)

hg38

Number of total reads
38759327
Reads aligned (%)
52.7
Duplicates removed (%)
31.4
Number of peaks
4401 (qval < 1E-05)

Base call quality data from DBCLS SRA