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Interferons inhibit Ebola virus infection of human keratinocytes

GSE309699 Homo sapiens (human) RNA-seq (gene expression) 44 samples Submitted 2025/10/04 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 44 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
44 samples: 10 conditions, mostly with about 4 replicates eachGroups 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
Interferons Inhibit Ebola Virus Infection of Human KeratinocytesViruses · 2025
Summary (written by the submitters)
Orthoebolavirus zairense, or Zaire Ebola virus (EBOV) is a species within the virus family Filoviridae, a group of viruses that can cause severe disease in humans characterized by hemorrhagic shock, coagulation abnormalities, and severe inflammation. While tissue macrophages are critical targets early during EBOV infection, other cell types support viral replication as disease progresses.
Read the full summary ↓
At late stages of infection, infectious EBOV is found on the surface of the skin, which may be a critical source of infectious virus transmitted be-tween individuals during outbreaks. Human skin contains a number of cellular targets of EBOV, including keratinocytes. Here, we demonstrate EBOV infection of telomer-ase-immortalized normal human skin keratinocytes (NHSK-1) as well as EBOVΔVP30 in-fection of NHSK-1 cells that were stably complemented with the EBOV transcription factor VP30. Infection with EBOVΔVP30 did not elicit detectable endogenous interferon re-sponses, however, exogenous pre-treatment of NHSK-1 cells with type I, II, and III inter-feron (IFN) inhibited EBOVΔVP30 infection and infection of an additional low contain-ment model of EBOV, rVSV/EBOV GP, in a dose-dependent manner. Analysis of the transcriptome of IFN-treated keratinocytes identified multiple genes unique to each IFN and a subset of ISGs upregulated by each IFN. Our results indicate that ISGs induced by IFN pre-treatment of keratinocytes can reduce infection, underlining possible anti-EBOV ISGs for development of EBOV-targeting therapeutics.
Published in
Interferons Inhibit Ebola Virus Infection of Human Keratinocytes
Elliff J, Van Ert H, Sevcik K et al. · Viruses 2025 · PMID 41472248 · doi:10.3390/v17121577
This dataset
Open GSE309699 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 GSE309699_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 PRJNA1336775 and SRA study SRP630134. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41472248) ↗
Study design
10 conditions, mostly with about 4 replicates each
NHSK-1 Cells, no IFN treatment, experiment 2, ×8 NHSK-1 Cells, no IFN treatment, experiment 1, ×7 NHSK-1 Cells, 6 hour IFN alpha treatment ×4 NHSK-1 Cells, 24 hour IFN alpha treatment ×4 NHSK-1 Cells, 6 hour IFN beta treatment ×4 NHSK-1 Cells, 24 hour IFN beta treatment ×4 NHSK-1 Cells, 6 hour IFN lambda treatment ×4 NHSK-1 Cells, 24 hour IFN lambda treatment ×4 +2 more

Supports a between-group comparison across 44 samples.

How we read this: 10 replicated groups read from 44 sample titles; they account for 44 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

+ 4 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

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