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Micronanoparticled risedronate exhibits potent vaccine adjuvant effects [RNA-Seq]

GSE239643 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/08/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 6 conditions, mostly in duplicateGroups 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)
Nanoparticles and microparticles are widely used as vaccine adjuvants to enhance the immune response and improve the stability of antigens. While aluminum salt is one of the most common adjuvants approved for human use, its immunostimulatory capacity is suboptimal. In this study, we modified risedronate, an immunostimulant and anti‐osteoporotic drug, to create the zinc salt particle-based risedronate (Zn-RS), also termed particulate risedronate.
Read the full summary ↓
Compared to soluble risedronate, the Zn-RS adjuvant demonstrated increased recruitment of innate cells, enhanced antigen uptake locally, and a similar antigen depot effect as aluminum salt. Furthermore, the Zn-RS adjuvant directly and quickly stimulated immune cells, accelerated the formulation of germinal centers in the lymph nodes, and facilitated the rapid production of antibodies. Importantly, the Zn-RS adjuvant exhibited superior performance in both young and aged mice, effectively protecting against respiratory diseases such as SARS-CoV-2 infection. Consequently, particulate risedronate showed great potential as a universal vaccine adjuvant, particularly beneficial for vaccines targeting the susceptible elderly.
This dataset
Open GSE239643 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 GSE239643_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 PRJNA1000477 and SRA study SRP452328. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in duplicate
6 weeks female mouse muscle, treated with S/A… ×2 6 weeks female mouse muscle, treated with S/Z… ×2 6 weeks female mouse muscle, treated with S/A… ×2 6 weeks female mouse muscle, treated with S/Z… ×2 6 weeks female mouse muscle, treated with S/A… ×2 6 weeks female mouse muscle, treated with S/Z… ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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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.