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Inducible POU2F3 expression in human intestinal organoids as a model of human tuft cells

GSE309917 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/05/27 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 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
Homo sapiens (human)
Samples
12 samples: 3 × intestinal organoids. J2 line, POU2F3 modified, uninduced, uninfected, biological replication vs 3 × intestinal organoids. J2 line, POU2F3 modified, uninduced, infected, biological replication vs 3 × intestinal organoids. J2 line, POU2F3 modified, induced, uninfected, biological replication vs 3 × intestinal organoids. J2 line, POU2F3 modified, induced, infected, biological replicationGroups 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
Inducible POU Class 2 Homeobox 3 Expression in Human Intestinal Organoids as a Model of Human Tuft CellsCellular and molecular gastroenterology and hepatology · 2026
Summary (written by the submitters)
Background & Aims: Tuft cells are relatively rare specialized chemosensory cells present in the intestinal epithelium. In mice, the intestinal tuft cell population expands in response to parasitic infection and stimulates the anti-parasitic immune response via cytokine signaling. However, elucidating the role of human intestinal tuft cells in homeostasis and disease remains has remained difficult due to their rarity in vivo and the lack of in vitro models.
Read the full summary ↓
Methods: We genetically engineered human intestinal organoids (HIOs) to express POU2F3, a transcription factor that drives tuft cell specification, and created an HIO that is approximately 40% tuft cell composition. Results: Human tuft cells generated in vitro express known tuft cell-specific transcripts (AVIL, TRPM5, ALOX5, PLCG2) as well as exhibit characteristics in vivo tuft morphology. Organoids with tuft cells exhibit transcriptional signatures that suggest WNT signaling and the presence of non-motile cilium. The tuft cells were infectable with human rotavirus, which has recently been shown to be a new target of rotavirus infection in the intestine. Conclusions: The expression of POU2F3 in HIOs results in a novel model system for functional studies of human intestinal tuft cells.
Published in
Inducible POU Class 2 Homeobox 3 Expression in Human Intestinal Organoids as a Model of Human Tuft Cells
Bomidi C, Wang L, Nguyen-Phuc H et al. · Cellular and molecular gastroenterology and hepatology 2026 · PMID 41956399 · doi:10.1016/j.jcmgh.2026.101784
This dataset
Open GSE309917 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 GSE309917_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 PRJNA1363986 and SRA study SRP644546. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41956399) ↗
Study design
3 × intestinal organoids. J2 line, POU2F3 modified, uninduced, uninfected, biological replication vs 3 × intestinal organoids. J2 line, POU2F3 modified, uninduced, infected, biological replication vs 3 × intestinal organoids. J2 line, POU2F3 modified, induced, uninfected, biological replication vs 3 × intestinal organoids. J2 line, POU2F3 modified, induced, infected, biological replication

Supports a between-group comparison across 12 samples.

How we read this: 4 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
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