GEO series

Murine pancreatic tumors induce pathological remodeling of muscles critical to chewing and swallowing [RNA-seq]

GSE336280 Mus musculus (mouse) RNA-seq (gene expression) 13 samples Submitted 2026/07/30 Platform GPL34328

At a glance

RNA-seq (gene expression) · mouse · 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: Mus musculus (mouse)
Samples: 13 samples: 3 × Digastric muscle, Sham/Control, vs 2 × Digastric muscle, KPC, vs 2 × Masseter muscle, Sham/Control, vs 2 × Masster muscle, Sham/Control,Groups 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.

Summary (written by the submitters)

Cancer cachexia is a debilitating syndrome defined by involuntary weight loss due to loss of muscle mass, with or without loss of fat mass. Cachexia is particularly prevalent in pancreatic cancer, affecting up to 70% of patients at diagnosis, and is associated with reduced physical function, impaired treatment tolerance, and worsened survival.

Read the full summary ↓

Skeletal muscle, including muscles involved in respiration and locomotion, exhibit extensive pathological remodeling in cachexia, including myofiber atrophy and transcriptional reprogramming. Whether muscles that are critical to chewing and swallowing respond similarly remains unknown. To address this gap, we collected masseter (chewing) and digastric (swallowing) muscles from cachectic mice bearing orthotopic KPC pancreatic tumors (n=8) and cancer-free Sham controls (n=8). Hematoxylin and eosin staining revealed increased mononuclear cell content, centralized nuclei, and expanded interstitial spaces in both muscles of KPC mice. Myofiber cross-sectional area was reduced by 42% in the masseter and 23% in the digastric. RNA sequencing revealed distinct transcriptional responses between these muscles. The masseter muscle showed enrichment of catabolic signaling pathways, including proteolytic and stress-response programs, alongside downregulation of extracellular matrix and growth-related programs. In contrast, the digastric muscle exhibited robust upregulation of immune and inflammatory pathways, including innate and adaptive immune signaling, with minimal overlap between muscles. Collectively, these findings demonstrate that pancreatic cancer drives pathological remodeling and atrophy in muscles central to chewing and swallowing while eliciting distinct, muscle-specific transcriptional responses, changes that could negatively affect food and nutrient intake and thereby contribute to cachexia progression.

This dataset

Open GSE336280 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 GSE336280_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 PRJNA1481200 and SRA study SRP711885. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × Digastric muscle, Sham/Control, vs 2 × Digastric muscle, KPC, vs 2 × Masseter muscle, Sham/Control, vs 2 × Masster muscle, Sham/Control,

Supports a between-group comparison across 9 samples.

How we read this: 4 replicated groups read from 13 sample titles; they account for 9 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

GSM9831292 Digastric muscle, Sham/Control, rep 1 Digastric muscle, Sham/…
GSM9831293 Digastric muscle, Sham/Control, rep 2 Digastric muscle, Sham/…
GSM9831294 Digastric muscle, Sham/Control, rep 3 Digastric muscle, Sham/…
GSM9831295 Digastric muscle, KPC, rep 1 Digastric muscle, KPC,
GSM9831296 Digastric muscle, KPC rep 2
GSM9831297 Digastric muscle, KPC, rep 3 Digastric muscle, KPC,
GSM9831298 Masseter muscle, Sham/Control, rep 1 Masseter muscle, Sham/C…
GSM9831299 Masseter muscle, Sham/Control, rep 2 Masseter muscle, Sham/C…
GSM9831300 Masster muscle, Sham/Control, rep 3 Masster muscle, Sham/Co…
GSM9831301 Masster muscle, Sham/Control, rep 4 Masster muscle, Sham/Co…
GSM9831302 Masseter muscle, KPC, rep 1
GSM9831303 Masseter muscle, KPC rep 2
GSM9831304 Masster muscle, KPC, rep 3

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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.