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Transplant immunosuppressant therapies induce unique functional changes in and re-shape gut immune homeostasis

GSE288074 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2025/06/24 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 10 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)
Current immunosuppressants effectively suppress adaptive and innate immune responses, but their broad, antigen-non-specific effects often result in significant complications. Here we investigated understudied immunosuppressant effects of four major immunosuppressant classes including tacrolimus, prednisone, mycophenolate mofetil (MMF), and Fingolimod (FTY), on the gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking.
Read the full summary ↓
Despite their distinct mechanisms of action, all drugs induced progressive alterations from moderate early changes to substantial alterations in the gut microbiome composition and metabolic pathways with prolonged treatment, converging to a shared dysbiotic state. This was accompanied by significant metabolic alterations and distinct phases of intestinal transcriptional responses. Time-dependent changes in lymph node (LN) reorganization and cellular composition were also observed, showing compartmentalized immune regulation in mesenteric and peripheral lymphoid tissues. Together, these findings highlight the underappreciated complexity and temporal dynamics of immunosuppressant effect, linking drug-induced changes in gut microbiome and compartmentalized immune regulation in lymphoid tissues. Notably, MMF and FTY demonstrated most robust immunomodulatory properties, and were able to suppress alloantigen-induced inflammation through mediating regulatory T cells and LN remodeling. Understanding these relationships provides new opportunities for refining immunosuppressive strategies to mitigate treatment-related complications in transplant patients, ultimately improving long-term organ transplant outcomes.
This dataset
Open GSE288074 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 GSE288074_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 PRJNA1215996 and SRA study SRP560033. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 conditions, mostly in triplicate
Control,D7, ×3 FTY,D7, ×3 MMF,D7, ×3 Pred,D7, ×3 Tac,D7, ×3 Control,D30, ×3 FTY,D30, ×3 MMF,D30, ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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.