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Novel lipid nanoparticle adjuvants vaccine for porcine reproductive and respiratory syndrome (PRRS) using in-vitro macrophage assays

GSE246438 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2025/10/25 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 12 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)
A novel triple adjuvant (TriAdj) platform formulated in various cationic lipid nanoparticles (L-TriAdj) was tested in-vitro for use in porcine reproductive and respiratory syndrome virus (PRRSV) vaccines. Gene expression changes in a RAW 264.7 macrophage cell line were evaluated (compared to media control) after 12-hour stimulation with: (i) TriAdj alone, (ii) lipid formulations alone, (iii) L-TriAdj (lipid:TriAdj ratio of 3:2 or 2:1), and (iv) L-TriAdj + PRRSV antigen.
Read the full summary ↓
Tested L-TriAdj formulations were comprised of (i) dimethyldioctadecylammonium bromide (DDAB) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) in a 55:45 ratio (abbreviated as DDAB/DOPE), or (ii) DDAB/DOPE with 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), and cholesterol in a 40:30:20:10 ratio (abbreviated as DDAB/DOPE/DSPC/CHOL).
This dataset
Open GSE246438 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 GSE246438_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 PRJNA1032933 and SRA study SRP468859. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
Control, ×3 45), ×3 45) + PRRSV, ×3 45) + TriAdj (2:1), ×3 45) + TriAdj (3:2), ×3 45) + TriAdj (2:1) + PRRSV, ×3 30:20:10), ×3 30:20:10) + PRRSV, ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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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