Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX2

Cell type

Cell type Class
Digestive tract
Cell type
KYSE-70
Primary Tissue
Esophagus
Tissue Diagnosis
Carcinoma Squamous Cell

Attributes by original data submitter

Sample

source_name
KYSE70_SOX2_AF2018
cell lines
KYSE70
antibody
SOX2
antibody vendor
R&D (AF2018)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinked with 1% formaldehyde, washed with PBS, lysed in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), sonicated with Covaris E210 to shear DNA to 200-1500bp. After immunoprecipitation or without immunoprecipitation for input, beads were washed, RNase A and Proteinase K treated and reverse crosslinked in elution buffer (1% SDS, 0.1M NaHCO3). DNAs were column purified and subjected to standard Illumina library construction.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
25321838
Reads aligned (%)
93.3
Duplicates removed (%)
5.0
Number of peaks
1687 (qval < 1E-05)

hg38

Number of total reads
25321838
Reads aligned (%)
95.4
Duplicates removed (%)
3.6
Number of peaks
2522 (qval < 1E-05)

Base call quality data from DBCLS SRA