GEO series

Mosquito- and tick-borne orthoflavivirus infections dysregulate microcephaly-associated genes in human neural progenitor cells

GSE309623 Homo sapiens (human) RNA-seq (gene expression) 45 samples Submitted 2026/04/02 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 45 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: 45 samples: 15 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.

Summary (written by the submitters)

Human neural progenitor cell (hNPC) transcriptomic responses to infections with Zika virus (ZIKV), Powassan virus (POWV), or two strains of West Nile virus were analyzed at three times after infection in a single batch of hNPCs differentiated from induced pluripotent stem cells. The WNV infections displayed the fastest replication kinetics but the POWV infection produced the highest viral yield.

Read the full summary ↓

All four infections upregulated common and unique innate immune and antiviral response genes by 12 hpi and induced upregulation of stress pathway genes by 24 hpi. The WNV infections downregulated cell cycle genes earlier than the ZIKV or POWV infections. Transcription factors regulating gene expression changes were predicted. All four orthoflaviviruses dysregulated the expression of 262 microcephaly-associated genes, with virus-specific differences in the extent of dysregulation. The data suggest that fetal hNPC infection in utero by each of the four orthoflaviviruses studied could induce neurodevelopmental disorders.

This dataset

Open GSE309623 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 GSE309623_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 PRJNA1336626 and SRA study SRP629967. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

15 conditions, mostly in triplicate

hNPCs, Mock, 12h, ×3 hNPCs, ZIKV, 12h, ×3 hNPCs, POWV, 12h, ×3 hNPCs, WNV MAD78, 12h, ×3 hNPCs, WNV NY99, 12h, ×3 hNPCs, Mock, 24h, ×3 hNPCs, ZIKV, 24h, ×3 hNPCs, POWV, 24h, ×3 +7 more

Supports a between-group comparison across 45 samples.

How we read this: 15 replicated groups read from 45 sample titles; they account for 45 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

GSM9270628 hNPCs, Mock, 12h, rep1 hNPCs, Mock, 12h,
GSM9270629 hNPCs, Mock, 12h, rep2 hNPCs, Mock, 12h,
GSM9270630 hNPCs, Mock, 12h, rep3 hNPCs, Mock, 12h,
GSM9270631 hNPCs, ZIKV, 12h, rep1 hNPCs, ZIKV, 12h,
GSM9270632 hNPCs, ZIKV, 12h, rep2 hNPCs, ZIKV, 12h,
GSM9270633 hNPCs, ZIKV, 12h, rep3 hNPCs, ZIKV, 12h,
GSM9270634 hNPCs, POWV, 12h, rep1 hNPCs, POWV, 12h,
GSM9270635 hNPCs, POWV, 12h, rep2 hNPCs, POWV, 12h,
GSM9270636 hNPCs, POWV, 12h, rep3 hNPCs, POWV, 12h,
GSM9270637 hNPCs, WNV MAD78, 12h, rep1 hNPCs, WNV MAD78, 12h,
GSM9270638 hNPCs, WNV MAD78, 12h, rep2 hNPCs, WNV MAD78, 12h,
GSM9270639 hNPCs, WNV MAD78, 12h, rep3 hNPCs, WNV MAD78, 12h,
GSM9270640 hNPCs, WNV NY99, 12h, rep1 hNPCs, WNV NY99, 12h,
GSM9270641 hNPCs, WNV NY99, 12h, rep2 hNPCs, WNV NY99, 12h,
GSM9270642 hNPCs, WNV NY99, 12h, rep3 hNPCs, WNV NY99, 12h,
GSM9270643 hNPCs, Mock, 24h, rep1 hNPCs, Mock, 24h,
GSM9270644 hNPCs, Mock, 24h, rep2 hNPCs, Mock, 24h,
GSM9270645 hNPCs, Mock, 24h, rep3 hNPCs, Mock, 24h,
GSM9270646 hNPCs, ZIKV, 24h, rep1 hNPCs, ZIKV, 24h,
GSM9270647 hNPCs, ZIKV, 24h, rep2 hNPCs, ZIKV, 24h,
GSM9270648 hNPCs, ZIKV, 24h, rep3 hNPCs, ZIKV, 24h,
GSM9270649 hNPCs, POWV, 24h, rep1 hNPCs, POWV, 24h,
GSM9270650 hNPCs, POWV, 24h, rep2 hNPCs, POWV, 24h,
GSM9270651 hNPCs, POWV, 24h, rep3 hNPCs, POWV, 24h,
GSM9270652 hNPCs, WNV MAD78, 24h, rep1 hNPCs, WNV MAD78, 24h,
GSM9270653 hNPCs, WNV MAD78, 24h, rep2 hNPCs, WNV MAD78, 24h,
GSM9270654 hNPCs, WNV MAD78, 24h, rep3 hNPCs, WNV MAD78, 24h,
GSM9270655 hNPCs, WNV NY99, 24h, rep1 hNPCs, WNV NY99, 24h,
GSM9270656 hNPCs, WNV NY99, 24h, rep2 hNPCs, WNV NY99, 24h,
GSM9270657 hNPCs, WNV NY99, 24h, rep3 hNPCs, WNV NY99, 24h,
GSM9270658 hNPCs, Mock, 48h, rep1 hNPCs, Mock, 48h,
GSM9270659 hNPCs, Mock, 48h, rep2 hNPCs, Mock, 48h,
GSM9270660 hNPCs, Mock, 48h, rep3 hNPCs, Mock, 48h,
GSM9270661 hNPCs, ZIKV, 48h, rep1 hNPCs, ZIKV, 48h,
GSM9270662 hNPCs, ZIKV, 48h, rep2 hNPCs, ZIKV, 48h,
GSM9270663 hNPCs, ZIKV, 48h, rep3 hNPCs, ZIKV, 48h,
GSM9270664 hNPCs, POWV, 48h, rep1 hNPCs, POWV, 48h,
GSM9270665 hNPCs, POWV, 48h, rep2 hNPCs, POWV, 48h,
GSM9270666 hNPCs, POWV, 48h, rep3 hNPCs, POWV, 48h,
GSM9270667 hNPCs, WNV MAD78, 48h, rep1 hNPCs, WNV MAD78, 48h,

+ 5 more — browse all 45 samples with per-sample file links →

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