Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX2

Cell type

Cell type Class
Lung
Cell type
NCI-H520
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma Squamous Cell

Attributes by original data submitter

Sample

source_name
H520_Sox2
cell line
NCI-H520
cell type
lung squamous cell carcinoma (LUSC) cell lines
chip antibody
Sox2 (R&D, AF2018)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For H3K27ac, Sox2 and p63 ChIP, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies. For Brn2 ChIP, cells were cross-linked with disuccinimidyl glutarate and formaldehyde. Nuclei were extracted, digested with micrococcal nuclease and sonicated. Then, histone-DNA complexes were isolated with ant-Brn2 antibody. Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer's protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 500 with paired-end 75bp reads.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
3953332
Reads aligned (%)
165.1
Duplicates removed (%)
3.5
Number of peaks
1060 (qval < 1E-05)

hg38

Number of total reads
3953332
Reads aligned (%)
166.5
Duplicates removed (%)
3.4
Number of peaks
1069 (qval < 1E-05)

Base call quality data from DBCLS SRA