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Pancreatic gene expression patterns during PDAC development in mice

GSE290898 Mus musculus (mouse) RNA-seq (gene expression) 35 samples Submitted 2025/11/25 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 35 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
35 samples: 5 conditions, mostly with about 11 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
Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancersCell reports. Medicine · 2026
Summary (written by the submitters)
This is a bulk RNA sequencing dataset of pancreatic tumors of varying disease grades from genetically engineered PDAC-bearing KPC mice (Pdx-1+/Cre; Kras+/LSL-G12D; Trp53+/LSL-R172H) (n = 24), and healthy controls (n = 11). KPC-derived tissues comprised early PDAC (only pancreatic remodeling and/or preinvasive lesions) to advanced disease (PDAC grades 2, 3, and 4).
Read the full summary ↓
Mice resulting from KPC strain breeding, which did not carry Pdx-1+/Cre but only Kras+/LSL-G12D and/or Trp53+/LSL-R172H-mutations, or which carried no mutation at all, served as control animals. To identify the changes in pancreatic gene expression during PDAC development, bulk RNAseq was performed on harvested pancreatic tissues.
Published in
Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers
Frädrich J, Reyes CM, Hendel M et al. · Cell reports. Medicine 2026 · PMID 41564862 · doi:10.1016/j.xcrm.2025.102546
This dataset
Open GSE290898 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 GSE290898_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 PRJNA1230726 and SRA study SRP567442. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41564862) ↗
Study design
5 conditions, mostly with about 11 replicates each
Control Pancreas, mouse ×11 KPC Pancreas, grade 3, mouse ×9 KPC Pancreas, early PDAC, mouse ×8 KPC Pancreas, grade 4, mouse ×4 KPC Pancreas, grade 2, mouse ×3

Supports a between-group comparison across 35 samples.

How we read this: 5 replicated groups read from 35 sample titles; they account for 35 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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