GEO series

Comparative Analysis of Caco-2 Cells and Human Jejunal and Duodenal Enteroid-derived Cells in Gel- and Membrane-Based Barrier Models of Intestinal Permeability

GSE276369 Homo sapiens (human) RNA-seq (gene expression) 13 samples Submitted 2025/04/02 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 13 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: 13 samples: 13 samples, each with a distinct title — no replicated groupsGroups 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: Comparative analysis of Caco-2 cells and human jejunal and duodenal enteroid-derived cells in gel- and membrane-based barrier models of intestinal permeabilityToxicological sciences : an official journal of the Society of Toxicology · 2025

Summary (written by the submitters)

Studies of gut absorption are necessary for characterization of drug toxicokinetics. While the human colon carcinoma cell line Caco-2 is the most used in vitro model, additional options have been proposed to represent different intestinal segments. Accordingly, we characterized the morphology and tissue specific marker expression of three human intestinal cell types: Caco-2 and primary human enteroid cells from jejunum (J2) and duodenum (D109).

Read the full summary ↓

Cells were cultured in the OrganoPlate® 3-lane 40 microphysiological system with flow (MPS) or static 24-well Transwells™. In both formats, J2 and D109 cells formed domedlike structures compared to uniform monolayers of Caco-2 cells. In the MPS, only Caco-2 cells formed uniform tubules. Cells grown on Transwells formed a thicker monolayer than in the MPS, with the most notable difference observed using J2 cells. All cells and culture conditions exhibited robust expression of ZO-1 (tight junctions). For cell polarization markers ezrin and villin, cell staining showed that expression was greatest in J2 and D109 cells cultured in the MPS. Regarding the functional marker mucin, J2 cells exhibited the highest expression, regardless of the platform. J2 and D109 cells exhibited poor barrier (70 kDa FITCTRITC-dextran) in MPS, but the tight barriers formed in Transwells. Barrier function and drug transport were also evaluated using caffeine, indomethacin, and propranolol; these compounds showed no appreciable binding to empty MPS or Transwells. Notably, we found that the gel lane in MPS was a sink for these compounds; only a small fraction (~13% over 15 hrs) crossed into the opposite channel, even without cells present. The permeability ratios among cell types in the MPS and Transwells were used to parameterize the probabilistic environmental compartmental absorption and transit model to determine whether in vitro data could reduce uncertainty in predictions. We found that the most accurate prediction of the fraction absorbed was achieved when using Transwell-derived data (Papp) from Caco-2 cells, combined with the experimentally-derived segment-specific (Caco-2, J2, and D109 data) absorption ratios. Overall, we show that marker staining was highest in enteroid-derived cells cultured in the MPS platform, but that studies of drug permeability across cell barriers in this model are challenging.

Published in

Comparative analysis of Caco-2 cells and human jejunal and duodenal enteroid-derived cells in gel- and membrane-based barrier models of intestinal permeability

Moyer HL, Vergara L, Stephan C et al. · Toxicological sciences : an official journal of the Society of Toxicology 2025 · PMID 39886939 · doi:10.1093/toxsci/kfaf011

This dataset

Open GSE276369 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 GSE276369_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 PRJNA1156791 and SRA study SRP530515. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39886939) ↗

Study design

13 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 13 sample titles: 13 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

GSM8497223 A1-Caco-TW-Gut-R1_S1
GSM8497224 A2-Caco-TW-Gut-R2_S9
GSM8497225 A3-Caco-TW-Gut-R3_S17
GSM8497226 A8-D109-TW-Gut-R2_S57
GSM8497227 A9-D109-TW-Gut-R3_S65
GSM8497228 B1-Caco-Mim-Gut-R1_S2
GSM8497229 B2-Caco-Mim-Gut-R2_S10
GSM8497230 B3-Caco-Mim-Gut-R3_S18
GSM8497231 B4-J2-Mim-Gut-R1_S26
GSM8497232 B5-J2-Mim-Gut-R2_S34
GSM8497233 B6-J2-Mim-Gut-R3_S42
GSM8497234 B8-D109-Mim-Gut-R2_S58
GSM8497235 B9-D109-Mim-Gut-R3_S66

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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.