Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZIC2

Cell type

Cell type Class
Blood
Cell type
BCBL1
NA
NA

Attributes by original data submitter

Sample

source_name
TREx-F3H3-K-Rta BCBL-1 cells
pathogen
KSHV
tissue
peritoneal effusion
cell type
KSHV positive B cell lymphoma
passages
5~10
chip antibody
ZIC2 (Abcam, ab150404)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA was sonicated to an average size of ~300 bp using a Diagenode Bioruptor. Chromatin DNA from 1 X 108 cells was used per immunoprecipitation assay with 10 µg of ZIC2 antibody ChIP-enriched and input DNA samples were used to generate Illumina-compatible libraries with the KAPA LTP Library Preparation Kit (Kapa Biosystems, KR0453) according to manufacturer’s recommendations.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
49884626
Reads aligned (%)
35.7
Duplicates removed (%)
63.0
Number of peaks
2238 (qval < 1E-05)

hg38

Number of total reads
49884626
Reads aligned (%)
37.3
Duplicates removed (%)
61.7
Number of peaks
2064 (qval < 1E-05)

Base call quality data from DBCLS SRA