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Cell of origin and expression profiles of pseudomyxoma peritonei derived from the appendix

GSE266302 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2025/04/30 Platform GPL17303
At a glance

RNA-seq (gene expression) · human · 20 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
Homo sapiens (human)
Samples
20 samples: 20 samples, each with a distinct title — no replicated groupsGroups 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)
Pseudomyxoma peritonei (PMP) is a rare disease caused by mucin-producing tumors developed most frequently from the appendix. This disease shows distinct clinical features by the cancerous cells producing mucin in the abdominal cavity. Although frequent mutations in the KRAS and GNAS genes have been reported in PMP, gene expression profiles of the tumors remain to be fully clarified because of its rarity and the difficulties in collecting pure cancerous cells scattered with a large volume of mucins.
Read the full summary ↓
To disclose the molecular features of PMP cells, we performed RNA-seq analysis of ten PMPs and their matched non-tumorous colonic epithelium in combination with laser-microdissection. As a result, we identified a total of 5,747 differently expressed genes (DEGs) between the tumors and non-tumorous colonic epithelium. A cell-of-origin subtype analysis with nearest template prediction algorithm corroborated that PMP tumor cells belonged to the goblet cell subtype, suggesting that tumorous cells of PMP have a feature of differentiation to goblet cells. Interestingly, gene set enrichment analysis (GSEA) uncovered that the tumors were significantly associated with three ontology terms, namely epithelial mesenchymal transition (EMT), tumor necrosis factor-alpha (TNF-α), and angiogenesis. Comparison of gene expression profiles between disseminated peritoneal adenomucinosis (DPAM) and peritoneal mucinous adenocarcinomas (PMCA) identified a total of 687 DEGs. Additional GSEA revealed that ontology terms “G2M checkpoint” and “E2F targets” were significantly enriched in PMCA supporting the view that PMCA has more aggressive properties than DPAM. These data may be useful for the understanding of molecular characteristics of PMP.
This dataset
Open GSE266302 in finder → Find more human 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 GSE266302_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 PRJNA1106532 and SRA study SRP505044. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
20 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 10 samples read as cases, 10 as controls.

How we read this: Read from 20 sample titles: 20 distinct titles with little repetition. 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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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.