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Multi-tissue microphysiological system captures integrated responses to nutritional overload and metabolic therapy

GSE330098 Homo sapiens (human) RNA-seq (gene expression) 108 samples Submitted 2026/07/29 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 108 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
Homo sapiens (human)
Samples
108 samples: 84 distinct titles, 24 of them repeatedGroups 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
Inter-organ communication shapes human metabolic tissue states and resolves anti-diabetic drug response modes in a six-tissue microphysiological systembioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
This study used a human six-tissue microphysiological system to examine how shared multi-tissue interaction, graded nutrient exposure, and pharmacologic perturbation shape tissue-specific transcriptional programs relevant to systemic glucose regulation. The MOTIVE-6 platform integrated hiPSC-derived midbrain organoids, intestinal epithelium, liver organoids, pancreatic islets, visceral adipocytes, and skeletal muscle in a shared circulating media environment.
Read the full summary ↓
Bulk RNA-seq was performed on individual tissue compartments after four days of culture under Low, Mid, or High nutrient conditions, with additional High-nutrient conditions treated with metformin or semaglutide. Matched isolation cultures were used to distinguish transcriptional effects associated with multi-tissue interaction from those observed in independently cultured tissues. This dataset enables analysis of tissue-specific responses to inter-tissue signaling, nutrient state, and anti-diabetic drug exposure in a perfused human multi-tissue model.
Published in
Inter-organ communication shapes human metabolic tissue states and resolves anti-diabetic drug response modes in a six-tissue microphysiological system
McGilvrey M, Chew S, Siddiqui MF et al. · bioRxiv : the preprint server for biology 2026 · PMID 42244566 · doi:10.64898/2026.05.22.726943
This dataset
Open GSE330098 in finder → Find more human 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 GSE330098_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 PRJNA1462736 and SRA study SRP697989. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42244566) ↗
Study design
84 distinct titles, 24 of them repeated
adypocyte_interaction_normal_diet_batch2 ×2 adypocyte_interaction_normal_diet_batch3 ×2 neuron_interaction_normal_diet_batch2 ×2 neuron_interaction_normal_diet_batch3 ×2 gut_epith_interaction_normal_diet_batch2 ×2 gut_epith_interaction_normal_diet_batch3 ×2 islet_interaction_normal_diet_batch2 ×2 islet_interaction_normal_diet_batch3 ×2 +16 more

How we read this: Read from 108 sample titles: 84 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

+ 68 more — browse all 108 samples with per-sample file links →

Datasets on a similar topic

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