GEO series

Inflammatory Neuropathy in Mouse and Primate Models of Colorectal Cancer

GSE338763 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/07/17 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 samples: 8 conditions, mostly in triplicateGroups 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)

Colorectal cancer survivors are at increased risk of developing neurological issues, particularly peripheral neuropathy and chronic pain. Although pre-existing neuropathy is a risk factor for chronic pain, tumor-induced neuropathy has not been firmly established in pre-clinical models. Consistent with clinical observations, we show that mice with colorectal cancer develop peripheral neuropathy, which was associated with subtle locomotor deficits, without overt hypersensitivity.

Read the full summary ↓

We detected widespread differences in pro-inflammatory cytokines and lipid metabolites in peripheral nerves from tumor-bearing mice. Macrophage accumulation, myelin decompaction and ryanodine receptor oxidation were associated with dysfunctional calcium homeostasis and reduced spike amplitude in sensory neurons. Similar alterations in plasma inflammatory mediators and lipid metabolites were associated with neuropathy and macrophage accumulation in peripheral nerves of rhesus macaques with colorectal cancer. These findings suggest colorectal cancer is causally linked to a subacute form of chronic inflammatory demyelinating polyneuropathy across species, which may represent an under-reported, yet important risk factor for neurological dysfunction in colorectal cancer survivors.

This dataset

Open GSE338763 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 GSE338763_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 PRJNA1495836 and SRA study SRP718310. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in triplicate

BMDM Vehicle ×3 BMDM MC38 ×3 SC Vehicle ×3 SC MC38 ×3 BMDM Vehicle intact ×3 BMDM Vehicle Deple ×3 MC38 Vehicle intact ×3 MC38 Vehicle Deple ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM9881145 BMDM Vehicle 1 BMDM Vehicle
GSM9881146 BMDM Vehicle 2 BMDM Vehicle
GSM9881147 BMDM Vehicle 3 BMDM Vehicle
GSM9881148 BMDM MC38 1 BMDM MC38
GSM9881149 BMDM MC38 2 BMDM MC38
GSM9881150 BMDM MC38 3 BMDM MC38
GSM9881151 SC Vehicle 1 SC Vehicle
GSM9881152 SC Vehicle 2 SC Vehicle
GSM9881153 SC Vehicle 3 SC Vehicle
GSM9881154 SC MC38 1 SC MC38
GSM9881155 SC MC38 2 SC MC38
GSM9881156 SC MC38 3 SC MC38
GSM9881157 BMDM Vehicle intact 1 BMDM Vehicle intact
GSM9881158 BMDM Vehicle intact 2 BMDM Vehicle intact
GSM9881159 BMDM Vehicle intact 3 BMDM Vehicle intact
GSM9881160 BMDM Vehicle Deple 1 BMDM Vehicle Deple
GSM9881161 BMDM Vehicle Deple 2 BMDM Vehicle Deple
GSM9881162 BMDM Vehicle Deple 3 BMDM Vehicle Deple
GSM9881163 MC38 Vehicle intact 1 MC38 Vehicle intact
GSM9881164 MC38 Vehicle intact 2 MC38 Vehicle intact
GSM9881165 MC38 Vehicle intact 3 MC38 Vehicle intact
GSM9881166 MC38 Vehicle Deple 1 MC38 Vehicle Deple
GSM9881167 MC38 Vehicle Deple 2 MC38 Vehicle Deple
GSM9881168 MC38 Vehicle Deple 3 MC38 Vehicle Deple

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GSE223323 Enterocyte like differentiation defines metabolic gene signatures of CMS3 colorectal cancers and provides therapeutic vulnerability 148 samples shares colorectal
GSE295477 Wumei Wan Remodels the Tumor Immune Microenvironment via the IDO1-KYN-AHR Axis in AOM/DSS-Induced Colorectal Cancer Model. 15 samples shares colorectal
GSE294825 A plastic EMP1⁺ to LGR5⁺ cell state conversion as a therapeutic bypass to KRAS-G12D inhibition in metastatic colorectal cancer [RNA-Seq mouse] 12 samples shares colorectal
GSE276018 Integrated Multi-Omics Analysis Reveals Epigenetic and Sex-Specific Alterations in Colorectal Cancer Cachexia 88 samples shares colorectal
GSE310707 Colon-restricted Pten haploinsufficiency models PI3K pathway-driven invasion in human colorectal cancer 6 samples shares colorectal

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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.