GEO series

Dietary cholesterol causes inflammatory imbalance and exacerbates morbidity in mice infected with influenza A virus

GSE197986 Mus musculus (mouse) RNA-seq (gene expression) 54 samples Submitted 2025/03/03 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 54 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: 54 samples: 8 conditions, mostly with about 6 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.

Summary (written by the submitters)

Influenza is a common cause of pneumonia-induced hospitalization and death, but how host factors function to influence disease susceptibility or severity has not been fully elucidated. Cellular cholesterol levels may affect the pathogenesis of influenza infection as cholesterol is crucial for viral entry and replication, as well as immune cell proliferation and function.

Read the full summary ↓

But there is still conflicting evidence on the extent to which dietary cholesterol influences cholesterol metabolism. Here, we examined the effects of a high cholesterol diet in modulating the immune response to influenza A virus (IAV) infection in mice. Mice were fed a standard or a high cholesterol diet for five weeks before inoculation with mouse-adapted human IAV (Puerto Rico/8/1934), and tissues were collected at days 0, 4, 8, and 16 post-infection. Cholesterol-fed mice exhibited dyslipidemia characterized by increased levels of total serum cholesterol prior to infection and decreased triglycerides after infection. Cholesterol-fed mice also displayed increased morbidity compared to mice fed a control diet, which was neither a result of immunosuppression nor changes in viral load. Instead, transcriptomic analysis of the lungs revealed that dietary cholesterol caused upregulation of genes involved in viral-response pathways and leukocyte trafficking, which coincided with increased numbers of cytokine-producing CD4+ and CD8+ T cells and infiltrating dendritic cells. Morbidity as determined by percent weight loss was highly correlated with numbers of cytokine-producing CD4+ and CD8+ T cells as well as granulocytes. Taken together, hypercholesterolemia promoted IAV morbidity via exaggerated cellular immune responses that were independent of viral load.

This dataset

Open GSE197986 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 GSE197986_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 PRJNA813290 and SRA study SRP362746. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly with about 6 replicates each

D8 Cholesterol diet ×9 D8 Control diet ×9 D0 Cholesterol diet ×6 D16 Cholesterol diet ×6 D4 Cholesterol diet ×6 D0 Control diet ×6 D16 Control diet ×6 D4 Control diet ×6

Supports a between-group comparison across 54 samples.

How we read this: 8 replicated groups read from 54 sample titles; they account for 54 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

GSM5935299 D0 Cholesterol diet 1 D0 Cholesterol diet
GSM5935300 D0 Cholesterol diet 2 D0 Cholesterol diet
GSM5935301 D0 Cholesterol diet 3 D0 Cholesterol diet
GSM5935302 D0 Cholesterol diet 4 D0 Cholesterol diet
GSM5935303 D0 Cholesterol diet 5 D0 Cholesterol diet
GSM5935304 D0 Cholesterol diet 6 D0 Cholesterol diet
GSM5935305 D16 Cholesterol diet 4 D16 Cholesterol diet
GSM5935306 D16 Cholesterol diet 5 D16 Cholesterol diet
GSM5935307 D16 Cholesterol diet 6 D16 Cholesterol diet
GSM5935308 D16 Cholesterol diet 1 D16 Cholesterol diet
GSM5935309 D16 Cholesterol diet 2 D16 Cholesterol diet
GSM5935310 D16 Cholesterol diet 3 D16 Cholesterol diet
GSM5935311 D4 Cholesterol diet 1 D4 Cholesterol diet
GSM5935312 D4 Cholesterol diet 2 D4 Cholesterol diet
GSM5935313 D4 Cholesterol diet 3 D4 Cholesterol diet
GSM5935314 D4 Cholesterol diet 4 D4 Cholesterol diet
GSM5935315 D4 Cholesterol diet 5 D4 Cholesterol diet
GSM5935316 D4 Cholesterol diet 6 D4 Cholesterol diet
GSM5935317 D8 Cholesterol diet 5 D8 Cholesterol diet
GSM5935318 D8 Cholesterol diet 6 D8 Cholesterol diet
GSM5935319 D8 Cholesterol diet 7 D8 Cholesterol diet
GSM5935320 D8 Cholesterol diet 8 D8 Cholesterol diet
GSM5935321 D8 Cholesterol diet 9 D8 Cholesterol diet
GSM5935322 D8 Cholesterol diet 1 D8 Cholesterol diet
GSM5935323 D8 Cholesterol diet 2 D8 Cholesterol diet
GSM5935324 D8 Cholesterol diet 3 D8 Cholesterol diet
GSM5935325 D8 Cholesterol diet 4 D8 Cholesterol diet
GSM5935326 D0 Control diet 1 D0 Control diet
GSM5935327 D0 Control diet 2 D0 Control diet
GSM5935328 D0 Control diet 3 D0 Control diet
GSM5935329 D0 Control diet 4 D0 Control diet
GSM5935330 D0 Control diet 5 D0 Control diet
GSM5935331 D0 Control diet 6 D0 Control diet
GSM5935332 D16 Control diet 1 D16 Control diet
GSM5935333 D16 Control diet 6 D16 Control diet
GSM5935334 D16 Control diet 2 D16 Control diet
GSM5935335 D16 Control diet 3 D16 Control diet
GSM5935336 D16 Control diet 4 D16 Control diet
GSM5935337 D16 Control diet 5 D16 Control diet
GSM5935338 D4 Control diet 1 D4 Control diet

+ 14 more — browse all 54 samples with per-sample file links →

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Search all mouse 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.