Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM4C

Cell type

Cell type Class
Neural
Cell type
SW 1783
Primary Tissue
Brain
Tissue Diagnosis
Astrocytoma

Attributes by original data submitter

Sample

source_name
SW1783 cells
cell line
SW1783
treatment
Wnt treatment
antibody
KDM4C antibody (Bethyl Laboratories, A300-885A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The method for chromatin immunoprecipitation was described as ChIP assay kit (Cell Signaling Technology), while the agarose beads were replaced by magnetic beads. Indexed libraries were prepared from 6ng-20ng of Diagenode Biorupter sheared ChIP DNA using the KAPA Hyper Library Preparation Kit (Kapa Biosystems, Inc).  Libraries were amplified by 6 cycles of PCR then assessed for quality using the Fragment Analyzer High Sensitivity NGS Fragment Analysis Kit (Advanced Analyticals) and quantified using the Qubit dsDNA HS Assay Kit (ThermoFisher).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
50461943
Reads aligned (%)
89.3
Duplicates removed (%)
6.9
Number of peaks
1114 (qval < 1E-05)

hg38

Number of total reads
50461943
Reads aligned (%)
92.0
Duplicates removed (%)
4.9
Number of peaks
4282 (qval < 1E-05)

Base call quality data from DBCLS SRA