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BULK RNAseq - SV40 large T antigen immortalization of primary mouse intestinal epithelial stem and progenitor cells

GSE298364 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2026/03/11 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 26 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
26 samples: 13 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
Development and characterization of immortalized mouse intestinal epithelial cell linesScientific reports · 2026
Summary (written by the submitters)
Developing new tools for studying the intestinal epithelium is essential for addressing unan-swered questions in development, physiology, and disease pathology. Primary intestinal epitheli-al stem cell (ISC) cultures are an invaluable in vitro model system. However, their cultivation re-mains technically demanding and costly, limiting their accessibility and use.
Read the full summary ↓
Though commonly utilized, most extant intestinal epithelial cell lines were derived from colon adenomas from vari-ous animals, are largely uncharacterized, and possess a plethora of genetic abnormalities, thus restricting rigor, reproducibility, and physiological relevance. Here we derived immortalized intestinal epithelial cell lines (iIECs) from six jejunal and six colonic stem cell-enriched spheroid cultures from wild type C57BL/6 mice. We transduced ISCs with a lentiviral vector encoding the SV40 large T antigen, and subsequently selected lines through adaptation to growth on plastic. Additionally, we weaned these lines off conditioned medium including the growth factors Wnt3a, Rspo3, and Noggin. We found that iIECs have growth characteristics similar to conventional plastic adapted cell lines. While we observed transcriptional signatures of epithelial-mesenchymal transition (EMT), these cells still exhibited epithelial characteristics including ex-pression of junctional proteins, mounted an innate immune response to viral infection, and se-creted cytokines in response to LPS stimulation. We further demonstrated the utility of iIECs through transient and stable genetic manipulation. iIECs occupy an important experimental niche through offering a scalable, practical, and physiologically relevant model system that can func-tion as a discovery platform before transitioning to primary spheroid cultures and/or animal models. We propose that they will be a valuable tool for advancing understanding of intestinal epithe-lial biology.
Published in
Development and characterization of immortalized mouse intestinal epithelial cell lines
Zhou JY, Espenschied ST, Lu Q et al. · Scientific reports 2026 · PMID 41673448 · doi:10.1038/s41598-026-38295-z
This dataset
Open GSE298364 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 GSE298364_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 PRJNA1269021 and SRA study SRP588369. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41673448) ↗
Study design
13 conditions, mostly in duplicate
ilEC_JA1_L ×2 ilEC_JA4_L ×2 ilEC_JC4_L ×2 ilEC_CA3_L ×2 ilEC_CA4_L ×2 ilEC_CB3_L ×2 Spheroid_WT8_jejunum_L ×2 Spheroid_WT9_jejunum_1_L ×2 +5 more

Supports a between-group comparison across 26 samples.

How we read this: 13 replicated groups read from 26 sample titles; they account for 26 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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