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Early spatiotemporal evolution of the immune response elicited by adenovirus vector vaccination

GSE264344 Mus musculus (mouse) RNA-seq (gene expression) 195 samples Submitted 2024/12/05 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 195 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
Mus musculus (mouse)
Samples
195 samples: 195 samples, each with a distinct title — no replicated groupsGroups 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
Early spatiotemporal evolution of the immune response elicited by adenovirus serotype 26 vector vaccination in micebioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
As the first responders to immunological challenges, the innate immune system has the potential to shape and regulate the ensuing adaptive immune response. Many clinical studies evaluating the role of various innate populations in initiating vaccine-elicited immunity have been largely relegated to blood. It is also largely unknown how the immune response to vaccination is initiating and evolving at the earliest time points post-vaccination.
Read the full summary ↓
We sought to investigate the spatiotemporal evolution of the earliest immune responses to intramuscular adenovirus serotype 26 (Ad26) vector vaccination in blood and tissues. Using transcriptomic profiling, we show that Ad26 vector vaccination elicits broad transcriptomic changes as early as 1 hour post-vaccination across blood and tissues marked by IL-1, TNF-α, and IL-6 pro-inflammatory pathways. Immunologic data reveals an influx of Ly6C+ myeloid cells into muscle by 1 hour post-vaccination. A Ly6C+CD64+ population emerges in muscle and subsequently in the draining lymph node, suggesting that myeloid cells may be significant drivers of vaccine-elicited immune responses following intramuscular vaccination. Moreover, levels of IL-6, MIG, MIP-1α, and MIP-1β measured in serum at 6 hours post-vaccination positively correlated with the frequency of vaccine-elicited CD8+ T cell responses evaluated at 60 days post-vaccination. Taken together, our data suggests that the immune response to Ad26 vector vaccination commences by 1 hour across compartments and that events at as early as 6 hours post-vaccination can shape vaccine-elicited CD8+ T cell responses at memory time points.
Published in
Early spatiotemporal evolution of the immune response elicited by adenovirus serotype 26 vector vaccination in mice
Blass E, Colarusso A, Aid M et al. · bioRxiv : the preprint server for biology 2024 · PMID 39464013 · doi:10.1101/2024.10.18.618988
This dataset
Open GSE264344 in finder → Find more mouse 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 GSE264344_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 PRJNA1102021 and SRA study SRP502699. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39464013) ↗
Study design
195 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 195 sample titles: 195 distinct titles with little repetition. 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

+ 155 more — browse all 195 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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