Antigen

Antigen Class

TFs and others

Antigen

Epitope tags

Cell type

Cell type Class

Blood

Cell type

BCBL1

NA

NA

Sample

source_name

TREx-(F3H3)-K-Rta BCBL-1 cells

tissue

human primary effusion lymphoma

cell type

KSHV-positive human B cell lymphoma cells

passages

5~10

chip antibody

FLAG M2 (Sigma, F1804)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Following treatment with doxycycline, cells (1 x 10^8) were fixed with formaldehyde, lysed, and chromatin DNA was sonicated to an average size of ~300 bp using a Diagenode Bioruptor. Chromatin immunoprecipitation (ChIP) of K-Rta-associated chromatin was performed with anti-FLAG M2 monoclonal antibody (10 ug). Subsequently, DNA was isolated with the QIAquick PCR Purification Kit (Qiagen) from the FLAG-K-RTa immunoprecipitates (ChIP DNA) and from input DNA controls. ChIP-enriched and input DNA samples (1 ng) were used to generate indexed, Illumina-compatible libraries with the KAPA LTP Library Preparation Kit (Kapa Biosystems, KK8230) according to manufacturer’s recommendations for end repair and A-tailing, adapter ligation, size selection, and library amplification.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

18677908

Reads aligned (%)

88.5

Duplicates removed (%)

30.0

Number of peaks

1073 (qval < 1E-05)

hg19

Number of total reads

18677908

Reads aligned (%)

87.5

Duplicates removed (%)

30.7

Number of peaks

1127 (qval < 1E-05)