← BioTransfer GEO Dataset Finder
GEO series

Gene expression dynamics in fibroblasts during early-stage murine pancreatic carcinogenesis

GSE270121 Mus musculus (mouse) RNA-seq (gene expression) 34 samples Submitted 2024/12/11 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 34 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
34 samples: 10 conditions, mostly with about 4 replicates eachGroups 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
Gene expression dynamics in fibroblasts during early-stage murine pancreatic carcinogenesisiScience · 2025
Summary (written by the submitters)
Pancreatic ductal adenocarcinoma (PDAC) stands as one of the most lethal malignancies, characterized by aggressive local tumor growth and metastatic spread, in part driven by fibroblast-mediated stromal reactions in the tumor microenvironment. Early detection is critical for improved patient outcomes. In this study, we investigate the molecular cues within fibroblasts that offer promise for early PDAC diagnosis.
Read the full summary ↓
We employ RNA sequencing of fibroblasts from KPC mouse models at pivotal time points, corresponding to the early preinvasive stages of pancreatic cancer. Our analysis reveals a substantial upregulation of gene sets associated with adipogenesis, fatty acid metabolism, and the ROS pathway in 12-week KPC-fibroblasts, indicative of metabolic reprogramming and redox regulation during early PDAC initiation. We narrow our focus to 26 potential key genes that may facilitate paracrine communication between fibroblasts and preneoplastic cells. Validation of our findings confirms the consistent increase in Angptl4, a gene linked to adipogenesis, and the notable downregulation of Lama2, a crucial extracellular matrix (ECM) gene. This study is the first to observe the elevation of Angptl4 in KPC-fibroblasts, providing essential insights into the role of fibroblasts in early PDAC. Moreover, our results hint at a potential role of fibroblasts in ECM degradation, a process that could support cancer cell proliferation and metastatic invasion. Genes associated with the ECM consistently display downregulation. These discoveries lay the foundation for future investigations into the mechanisms driving fibroblast-mediated elevation of Angptl4 and downregulation of ECM genes and their role in mediating crosstalk between fibroblast and preneoplastic cells. Our investigation into fibroblast transcriptional dynamics during early carcinogenesis offers significant potential for enhancing early diagnostic approaches in combating this deadly malignancy.
Published in
Gene expression dynamics in fibroblasts during early-stage murine pancreatic carcinogenesis
Ohri N, Häußler J, Javakhishvili N et al. · iScience 2025 · PMID 39811640 · doi:10.1016/j.isci.2024.111572
This dataset
Open GSE270121 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 GSE270121_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 PRJNA1125037 and SRA study SRP514494. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39811640) ↗
Study design
10 conditions, mostly with about 4 replicates each
KPC_8week ×4 KPC_6week ×4 Cre_8week ×4 Cre_6week ×4 Cre_4week ×4 KPC_10week ×3 KPC_12week ×3 KPC_4week ×3 +2 more

Supports a between-group comparison across 34 samples.

How we read this: 10 replicated groups read from 34 sample titles; they account for 34 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

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.