Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM4C

Cell type

Cell type Class
Digestive tract
Cell type
KYSE-150
Primary Tissue
Esophagus
Tissue Diagnosis
Carcinoma Squamous Cell

Attributes by original data submitter

Sample

source_name
KYSE150_shJMJD2C_JMJD2C
cell line
KYSE150
treatment
shJMJD2C
chip antibody
JMJD2C

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed using formaldehyde crosslinked chromatin sonicated to an average size of 200-600 bp and the indicated antibodies. 5-10 ng of DNA was processed using NEBNext and Illumina ChIP seq kits according to the manufacturer's instructions. In brief, DNA was adaptor-ligated, subjected to gel size selection, amplified and analyzed by Solexa/Illumina high-throughput sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
55742330
Reads aligned (%)
87.9
Duplicates removed (%)
9.8
Number of peaks
1480 (qval < 1E-05)

hg38

Number of total reads
55742330
Reads aligned (%)
90.0
Duplicates removed (%)
8.3
Number of peaks
1463 (qval < 1E-05)

Base call quality data from DBCLS SRA