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ZIKV infection series in paediaitric brain tumour and NPC cell lines

GSE277900 Homo sapiens (human) RNA-seq (gene expression) 61 samples Submitted 2025/04/23 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 61 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)
Topic
Nasopharyngeal carcinomaThis series is part of our curated briefing on it.
Samples
61 samples: 20 conditions, mostly in triplicateGroups 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
Multi-omics analysis reveals key immunogenic signatures induced by oncolytic Zika virus infection of paediatric brain tumour cellsScientific reports · 2025
Summary (written by the submitters)
Zika virus (ZIKV) is a mosquito-borne flavivirus consisting of historical African and epidemic-associated Asian lineages. The latter can access the central nervous system and causes microcephaly in the developing foetus through infection and depletion of neural stem and progenitor cells. The molecular mechanisms involved in this depletion response are grossly unknown for cells arising from CZS-affected children.
Read the full summary ↓
Since 2017, the concept of employing ZIKV as oncolytic virotherapy against brain tumours has gained momentum. Oncolytic virotherapy exploits viruses that preferentially infect and destroy cancer cells via two distinct routes of therapeutic action. Following infection, intense viral replication induces oncolysis, releasing virions into the tumour microenvironment to infect neighbouring tumour cells. ZIKV induces an oncolytic event in infected pediatric brain tumour cells, but the molecular mechanisms involved in this response are grossly unknown. Here, we sought to investigate the molecular mechanisms underlying both the oncolytic and neuropathogenic responses of ZIKV infection in brain tumour and NPCs, respectively.
Published in
Multi-omics analysis reveals key immunogenic signatures induced by oncolytic Zika virus infection of paediatric brain tumour cells
Sherwood M, Mitsugi TG, Kaid C et al. · Scientific reports 2025 · PMID 40240536 · doi:10.1038/s41598-025-97804-8
This dataset
Open GSE277900 in finder → Find more human RNA-seq datasets → Nasopharyngeal carcinoma landscape →
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 GSE277900_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 PRJNA1164726 and SRA study SRP534466. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40240536) ↗
Study design
20 conditions, mostly in triplicate
DAOY ZIKV infection 12 hours post infection ×3 DAOY ZIKV infection 18 hours post infection ×3 DAOY ZIKV infection 24 hours post infection ×3 DAOY uninfected ×3 Neural precursor cell 763-1 ZIKV infection 12… ×3 Neural precursor cell 763-1 ZIKV infection 18… ×3 Neural precursor cell 763-1 ZIKV infection 24… ×3 Neural precursor cell 763-1 uninfected ×3 +14 more

Supports a between-group comparison across 59 samples.

How we read this: 20 replicated groups read from 61 sample titles; they account for 59 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

+ 21 more — browse all 61 samples with per-sample file links →

More Nasopharyngeal carcinoma datasets

Search all human RNA-seq datasets in GEO →

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