GEO series

RNA seq analysis comparing uninfected to MCPyV-infected 2D monolayer or 3D spheroids

GSE311065 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/05/29 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 3 × EV 2D vs 3 × MCPyV 2D vs 3 × EV 3D vs 3 × MCPyV 3DGroups 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: Merkel cell polyomavirus exploits extracellular vesicles for skin infection and host immune evasion through activated Wnt signalingPLoS pathogens · 2026

Summary (written by the submitters)

Human tumor virus infections account for ~10% of the world’s cancer cases. However, studies on the life cycle of small DNA tumor viruses have been hampered primarily due to the lack of virus culture systems that allow for robust replication and high-level infection in host cells. Thus, studies involving Merkel cell polyomavirus (MCPyV), a human oncogenic polyomavirus, infections primarily rely on utilizing quasiviruses, virions produced through the artificial complementation of the viral genome with exogenous MCPyV proteins.

Read the full summary ↓

However, recombinant quasiviruses might not fully reflect the native MCPyV virions or infection conditions. To mimic the natural skin infection of MCPyV, we developed a simple and efficient method for producing MCPyV virions derived from primary human dermal fibroblasts without the requirement for exogenous MCPyV protein supplementation using a 3D spheroid culture system. Here, we found that the 3D spheroid microenvironment enabled the production of MCPyV virions and their release into the supernatant that were packaged inside of extracellular vesicles (EVs) from natural host cells. This demonstrates that the physical properties within the skin structure influence how MCPyV establishes a unique infectious life cycle by avoiding host immune surveillance. We propose the use of 3D spheroids as a novel cell culture system to recapitulate the MCPyV life cycle and establish a skin infection, a feature which has been challenging to accomplish in the field.

Published in

Merkel cell polyomavirus exploits extracellular vesicles for skin infection and host immune evasion through activated Wnt signaling

Pham AM, Ortiz LE, Chen H et al. · PLoS pathogens 2026 · PMID 42335122 · doi:10.1371/journal.ppat.1014360

This dataset

Open GSE311065 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 GSE311065_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 PRJNA1368622 and SRA study SRP648126. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42335122) ↗

Study design

3 × EV 2D vs 3 × MCPyV 2D vs 3 × EV 3D vs 3 × MCPyV 3D

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM9316368 EV 2D 1 EV 2D
GSM9316369 EV 2D 2 EV 2D
GSM9316370 EV 2D 3 EV 2D
GSM9316371 MCPyV 2D 1 MCPyV 2D
GSM9316372 MCPyV 2D 2 MCPyV 2D
GSM9316373 MCPyV 2D 3 MCPyV 2D
GSM9316374 EV 3D 1 EV 3D
GSM9316375 EV 3D 2 EV 3D
GSM9316376 EV 3D 3 EV 3D
GSM9316377 MCPyV 3D 1 MCPyV 3D
GSM9316378 MCPyV 3D 2 MCPyV 3D
GSM9316379 MCPyV 3D 3 MCPyV 3D

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