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A viral circular RNA in Kaposi’s sarcoma-associated herpesvirus contributes to viral and host gene expression during latent and lytic replication

GSE293213 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/06/04 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 10 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
10 samples: 3 × iSLK cells, wild-type virus, lytic infection, 72 hours, biol vs 3 × iSLK cells, delta_circ-vIRF4 mutant virus, lytic infection, 72 hours, biol vs 2 × iSLK cells, wild-type virus, latent infection, biol vs 2 × iSLK cells, delta_circ-vIRF4 mutant virus, latent infection, biolGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
A viral circular RNA in Kaposi's sarcoma-associated herpesvirus modulates viral and host gene expression during latent and lytic replicationExploration of targeted anti-tumor therapy · 2025
Summary (written by the submitters)
Aim: Circular RNA (circRNA) is a class of noncoding, single-stranded RNA generated by backsplicing, a process where the 5’ and 3’ ends of an RNA are covalently joined. Virally encoded circRNAs have been identified in several members of Gammaherpesvirinae, including Kaposi’s sarcoma-associated herpesvirus (KSHV). In KSHV, the viral interferon regulatory factor 4 (vIRF4) region produces two isoforms of circRNA (circ-vIRF4) that are detectable during latency and reactivation.
Read the full summary ↓
Since these circRNAs are expressed during latency, a period where viral transcription is tightly restricted and tumorigenesis occurs, circ-vIRF4 may contribute to the development of KSHV malignancies. Therefore, the aim of this study is to characterize the function of vIRF4 circRNAs. Methods: A KSHV mutant (Δcirc-vIRF4) was generated in the BAC16 bacmid and transfected into 293T and iSLK cells. Expression of circRNA after mutagenesis was assessed by qualitative and quantitative PCR. Host and viral gene expression in iSLK cells during both viral latency and reactivation were also assessed by RNA-seq. Results: RT-PCR of Δcirc-vIRF4-infected iSLK cells demonstrated no expression of wild type isoforms, but PCR cloning showed that alternative backsplice sites were used to express novel vIRF4 circRNAs, where the most prominent isoform was a 1,020 nt isoform. RNA-seq analyses comparing WT- and Δcirc-vIRF4-infected iSLK cells demonstrated significant differential expression of both host and viral genes during both phases of the viral life cycle. Gene ontology analyses returned terms related to cell adhesion, proliferation, and migration for both datasets, as well as kinase signaling and apoptosis for the lytic dataset. Conclusions: These results show that KSHV can switch to an alternative backsplice site for vIRF4 circRNA production in the absence of a canonical splice site and that circ-vIRF4 contributes to the regulation of both host and viral gene expression through an unknown mechanism.
Published in
A viral circular RNA in Kaposi's sarcoma-associated herpesvirus modulates viral and host gene expression during latent and lytic replication
Torres S, Jain V, Stribling D et al. · Exploration of targeted anti-tumor therapy 2025 · PMID 40452889 · doi:10.37349/etat.2025.1002320
This dataset
Open GSE293213 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE293213_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1243360 and SRA study SRP574057. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40452889) ↗
Study design
3 × iSLK cells, wild-type virus, lytic infection, 72 hours, biol vs 3 × iSLK cells, delta_circ-vIRF4 mutant virus, lytic infection, 72 hours, biol vs 2 × iSLK cells, wild-type virus, latent infection, biol vs 2 × iSLK cells, delta_circ-vIRF4 mutant virus, latent infection, biol

Supports a case/control comparison: 5 samples read as cases, 5 as controls.

How we read this: 4 replicated groups read from 10 sample titles; they account for 10 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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