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Transcriptomic profiling reveals substrate- and shear stress_x0002_dependent maturation of human small intestinal epithelial cells

GSE320151 Homo sapiens (human) RNA-seq (gene expression) 58 samples Submitted 2026/04/22 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 58 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
58 samples: 29 conditions, mostly in duplicateGroups 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
Transcriptomic profiling reveals substrate- and shear stress-dependent maturation of human small intestinal epithelial cellsFrontiers in pharmacology · 2026
Summary (written by the submitters)
Primary human intestinal epithelial cells (IECs) require microenvironments that reproduce various in vivo cues to maintain survival, differentiation, and function in vitro. In this study, we investigated how intestinal stem cell (ISC)-derived monolayers respond to biomimetic substrates and shear stress using 3D-printed hydrogels based on bioactive decellularized and methacrylated small intestinal submucosa (dSIS-MA) integrated into a custom millifluidic system.
Read the full summary ↓
Extensive bulk RNA sequencing experiments revealed that, compared with Matrigel-coated tissue culture plastic, dSIS-MA hydrogels supported survival- and differentiation-related signaling, stabilized gene expression over time, and promoted absorptive lineage maturation while reducing crypt-associated signatures. By applying dynamic culture conditions to the hydrogel system, IECs underwent transcriptional remodeling, characterized by activation of metabolic and immune pathways. Longitudinal analysis further indicated that shear stress enhanced metabolic pathway–associated gene expression and promoted differentiation toward absorptive lineages. These findings establish dSIS-MA hydrogels with controlled fluid flow as a biomimetic in vitro model that supports survival, maturation of human IECs and enables transcriptional adaptation to defined biochemical and mechanical cues, supporting future applications in disease modelling, drug testing, and regenerative medicine.
Published in
Transcriptomic profiling reveals substrate- and shear stress-dependent maturation of human small intestinal epithelial cells
Alzain N, Almalla A, Sandu K et al. · Frontiers in pharmacology 2026 · PMID 42147349 · doi:10.3389/fphar.2026.1706106
This dataset
Open GSE320151 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 GSE320151_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 PRJNA1426471 and SRA study SRP678507. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42147349) ↗
Study design
29 conditions, mostly in duplicate
Plastic_Day0_techRep1 ×2 Plastic_Day0_techRep2 ×2 Plastic_Day0_techRep3 ×2 Plastic_Day0_techRep4 ×2 Scaffold_Day0_techRep1 ×2 Scaffold_Day0_techRep2 ×2 Scaffold_Day0_techRep3 ×2 Plastic_Day1_techRep1 ×2 +21 more

Supports a between-group comparison across 58 samples.

How we read this: 29 replicated groups read from 58 sample titles; they account for 58 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

+ 18 more — browse all 58 samples with per-sample file links →

Datasets on a similar topic

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