GEO series

Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis

GSE314812 Homo sapiens (human) RNA-seq (gene expression) 55 samples Submitted 2026/02/23 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 55 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)
Topic: Gastric cancerThis series is part of our curated briefing on it.
Samples: 55 samples: 5 conditions, mostly in duplicateGroups 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)

Gastric cancer peritoneal metastasis (GCPM) is a distinct clinical entity with a poor prognosis, characterized by aggressive features and limited treatment options. Understanding its molecular biology is critical for developing effective therapies. We performed whole genome and transcriptome sequencing on GCPM samples and paired primary gastric cancer (GC) tissues from 14 and 26 patients, respectively.

Read the full summary ↓

Our analysis revealed substantial intra-patient heterogeneity between GCPM and primary tumors at both genetic and functional levels. Inter-patient variability was observed in mutational overlaps, with some signatures unique to either GCPM or primary tumors. Tumor evolution analysis suggested divergent clonal evolution, with distinct clones specific to GCPM or primary tumors in most patients. The tumor microenvironment (TME) was poorly conserved between primary GC and GCPM, with desert-type primary tumors often transitioning to immune-enriched TMEs in metastases. These findings suggest that immunotherapy resistance in GCPM may arise from factors beyond intrinsic TME characteristics, such as limited drug delivery due to the peritoneal-plasma barrier. Collectively, our results highlight significant molecular and TME heterogeneity between GCPM and primary tumors, emphasizing the need for GCPM-specific stratification and innovative treatment strategies to improve outcomes.

This dataset

Open GSE314812 in finder → Find more human RNA-seq datasets → Gastric cancer landscape →

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 GSE314812_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 PRJNA1392638 and SRA study SRP657479. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 conditions, mostly in duplicate

GC Peritoneal metastatic tumor, patient GC ×24 GC Primary tumor, patient GC ×17 NAT, patient GC ×6 GC Omentum metastatic tumor, patient GC ×2 GC Lymph node metastatic tumor, patient GC ×2 GC Primary tumor, patient GC05a ×1 GC Peritoneal metastatic tumor, patient GC05a ×1 GC Primary tumor, patient GC05b ×1 +1 more

Supports a between-group comparison across 51 samples.

How we read this: 5 replicated groups read from 55 sample titles; they account for 51 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

GSM9411046 GC Primary tumor, patient GC01 GC Primary tumor, patie…
GSM9411047 GC Peritoneal metastatic tumor, patient GC01 GC Peritoneal metastati…
GSM9411048 GC Primary tumor, patient GC02 GC Primary tumor, patie…
GSM9411049 GC Peritoneal metastatic tumor, patient GC02 GC Peritoneal metastati…
GSM9411050 GC Primary tumor, patient GC03 GC Primary tumor, patie…
GSM9411051 GC Peritoneal metastatic tumor, patient GC03 GC Peritoneal metastati…
GSM9411052 GC Peritoneal metastatic tumor, patient GC04 GC Peritoneal metastati…
GSM9411053 GC Primary tumor, patient GC05a
GSM9411054 GC Peritoneal metastatic tumor, patient GC05a
GSM9411055 GC Primary tumor, patient GC05b
GSM9411056 GC Peritoneal metastatic tumor, patient GC05b
GSM9411057 GC Primary tumor, patient GC06 GC Primary tumor, patie…
GSM9411058 GC Peritoneal metastatic tumor, patient GC06 GC Peritoneal metastati…
GSM9411059 GC Peritoneal metastatic tumor, patient GC07 GC Peritoneal metastati…
GSM9411060 GC Omentum metastatic tumor, patient GC07 GC Omentum metastatic t…
GSM9411061 NAT, patient GC08 NAT, patient GC
GSM9411062 GC Primary tumor, patient GC08 GC Primary tumor, patie…
GSM9411063 GC Lymph node metastatic tumor, patient GC08 GC Lymph node metastati…
GSM9411064 NAT, patient GC09 NAT, patient GC
GSM9411065 GC Primary tumor, patient GC09 GC Primary tumor, patie…
GSM9411066 GC Peritoneal metastatic tumor, patient GC09 GC Peritoneal metastati…
GSM9411067 NAT, patient GC10 NAT, patient GC
GSM9411068 GC Primary tumor, patient GC10 GC Primary tumor, patie…
GSM9411069 GC Peritoneal metastatic tumor, patient GC10 GC Peritoneal metastati…
GSM9411070 GC Primary tumor, patient GC11 GC Primary tumor, patie…
GSM9411071 GC Peritoneal metastatic tumor, patient GC11 GC Peritoneal metastati…
GSM9411072 GC Peritoneal metastatic tumor, patient GC12 GC Peritoneal metastati…
GSM9411073 GC Peritoneal metastatic tumor, patient GC13 GC Peritoneal metastati…
GSM9411074 GC Peritoneal metastatic tumor, patient GC14 GC Peritoneal metastati…
GSM9411075 NAT, patient GC15 NAT, patient GC
GSM9411076 GC Primary tumor, patient GC15 GC Primary tumor, patie…
GSM9411077 GC Peritoneal metastatic tumor, patient GC15 GC Peritoneal metastati…
GSM9411078 GC Primary tumor, patient GC16 GC Primary tumor, patie…
GSM9411079 GC Peritoneal metastatic tumor, patient GC16 GC Peritoneal metastati…
GSM9411080 GC Primary tumor, patient GC17 GC Primary tumor, patie…
GSM9411081 GC Peritoneal metastatic tumor, patient GC17 GC Peritoneal metastati…
GSM9411082 NAT, patient GC18 NAT, patient GC
GSM9411083 GC Primary tumor, patient GC18 GC Primary tumor, patie…
GSM9411084 GC Peritoneal metastatic tumor, patient GC18 GC Peritoneal metastati…
GSM9411085 GC Primary tumor, patient GC19 GC Primary tumor, patie…

+ 15 more — browse all 55 samples with per-sample file links →

More Gastric cancer datasets

GSE134520 Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer [10x genomics] 13 samples same disease briefing · shares gastric
GSE163558 Transcriptional heterogeneity in primary and metastatic gastric cancer revealed using single-cell RNA sequencing 10 samples same disease briefing · shares gastric
GSE173195 Roles of LTBP1 in the gastric cancer cells 6 samples same disease briefing · shares gastric
GSE182543 ALKBH5 cooperated with LINC00659 promote gastric cancer progression by JAK1 mRNA m6A-YTHDF2-dependent modification [polyA] 6 samples same disease briefing · shares gastric
GSE103045 Genetic and epigenetic gene inactivation coupling with KRAS activation in human gastric cancer [RNA-Seq] 3 samples same disease briefing · shares gastric
GSE119196 HOXC10 Overexpression Promotes Cell Proliferation and Migration through Regulation of CST1 Expression in Gastric Cancer 2 samples same disease briefing · shares gastric
GSE171054 NINJ2 inhibition increased chemo-sensitivity by decreasing CICs in chemotherapy-resistant gastric cancer 2 samples same disease briefing · shares gastric
GSE182542 ALKBH5 cooperated with LINC00659 promote gastric cancer progression by JAK1 mRNA m6A-YTHDF2-dependent modification [2-m6A] 2 samples same disease briefing · shares gastric

Search all human RNA-seq datasets in GEO →

Share this dataset

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.