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Transcriptomic profiling of Adjacents CAFs of MC38 tumor cells on murine MC38 liver metastasis sections by NanoString GeoMX DSP

GSE253938 Mus musculus (mouse) Spatial transcriptomics 27 samples Submitted 2025/06/11 Platform GPL30172
At a glance

Spatial transcriptomics · mouse · 27 samples

What it is
Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism
Mus musculus (mouse)
Samples
27 samples: 27 × CAF Kang4_002 |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.
Paper
CMTM6 mediates the Warburg effect and promotes the liver metastasis of colorectal cancerExperimental & molecular medicine · 2024
Summary (written by the submitters)
To study how targeting CMTM6 in CRCs influences the transcritome. Adjacents CAFs of Control MC38 and CMTM6-deficient MC38 were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP
Published in
CMTM6 mediates the Warburg effect and promotes the liver metastasis of colorectal cancer
Shaha A, Wang Y, Wang X et al. · Experimental & molecular medicine 2024 · PMID 39218981 · doi:10.1038/s12276-024-01303-1
This dataset
Open GSE253938 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 GSE253938_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1067714 and SRA study SRP485292. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39218981) ↗
Study design
27 × CAF Kang4_002 |

Supports a between-group comparison across 27 samples.

How we read this: 1 replicated groups read from 27 sample titles; they account for 27 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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