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RNA-Seq Time-Course Analysis of NPCs Transcriptome in Response to HSV-1 Infection

GSE236646 Homo sapiens (human) RNA-seq (gene expression) 53 samples Submitted 2024/07/31 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 53 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
53 samples: 6 conditions, mostly with about 9 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
RNA-Seq time-course analysis of neural precursor cell transcriptome in response to herpes simplex Virus-1 infectionJournal of neurovirology · 2024
Summary (written by the submitters)
The neurogenic niches within the central nervous system serve as essential reservoirs for neural precursor cells (NPCs), playing a crucial role in neurogenesis. However, these NPCs are particularly vulnerable to infection by the herpes simplex virus type 1 (HSV-1). In the present study, we investigated the changes in the transcriptome of NPCs in response to Herpes simplex virus 1 (HSV-1) infection. Using bulk RNA-Seq, the transcriptomes of HSV-1-infected NPCs were compared to those of uninfected samples at different time points in the presence or absence of antivirals.
Published in
RNA-Seq time-course analysis of neural precursor cell transcriptome in response to herpes simplex Virus-1 infection
Wood JA, Chaparala S, Bantang C et al. · Journal of neurovirology 2024 · PMID 38478163 · doi:10.1007/s13365-024-01198-8
This dataset
Open GSE236646 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 GSE236646_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 PRJNA991956 and SRA study SRP447866. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38478163) ↗
Study design
6 conditions, mostly with about 9 replicates each
infected at MOI 0.0001 + 5BVdU + IFN-alpha - … ×9 infected at MOI 0.0001 - Day ×9 infected at MOI 0.001 + 5BVdU + IFN-alpha - D… ×9 infected at MOI 0.001 - Day ×9 Uninfected - Day ×9 Uninfected + 5BVdU + IFN-alpha – Day ×8

Supports a between-group comparison across 53 samples.

How we read this: 6 replicated groups read from 53 sample titles; they account for 53 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

+ 13 more — browse all 53 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.