Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
VRK1

Cell type

Cell type Class
Bone
Cell type
HT-1080
Primary Tissue
Bone
Tissue Diagnosis
Fibrosarcoma

Attributes by original data submitter

Sample

source_name
fibrosarcoma
cell line
HT1080
chip antibody
anti-VRK1
sirna
siControl

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates derived from fixed and sonicated nuclei was immunoprecipitated by anti-H2ApT120, anti-H2AubK119 and anti-VRK1 antibody. To add single adenosine, DNA was treated with klewnow exo- (3’ and 5’ exo minus; Illumina). Illumina adaptors were added and subjected to 20 cycles of PCR amplification according to manufacturer's instructions. Purified DNA was subjected to cluster generation and 36 cycles of sequencing on the Illumina cluster station and Genome Analyzer following the manufacturer’s instractions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
40505644
Reads aligned (%)
96.0
Duplicates removed (%)
6.4
Number of peaks
616 (qval < 1E-05)

hg38

Number of total reads
40505644
Reads aligned (%)
96.9
Duplicates removed (%)
5.0
Number of peaks
533 (qval < 1E-05)

Base call quality data from DBCLS SRA