Spatial transcriptomics reveal lineage complexity of gastric incomplete intestinal metaplasia and its association with gastric cancers [scRNA-Seq]
Spatial transcriptomics · human · 10 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Homo sapiens (human)
- Samples
- 10 samples: 10 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.
- Paper
- Hybrid identity and distinct methylation profiles of incomplete intestinal metaplasia in the stomachGut · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE295401_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1254596 and SRA study SRP580893. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 sample titles: 10 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.
- GSM8947399 naGF
- GSM8947400 naBMP
- GSM8947401 IncomGF
- GSM8947402 IncomBMP
- GSM8947403 ComGF
- GSM8947404 ComBMP
- GSM8947405 SI
- GSM8947406 SIBMP
- GSM8947407 CN
- GSM8947408 CNBMP
- GSE210991 5' droplet-based single cell RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids [scRNA-seq] 29 samples shares intestinal, metaplasia, scrna-seq
- GSE210995 HKU Gastric Intestinal Metaplasia study: Single-cell RNA sequencing, transcriptome and methylation profiling 199 samples shares intestinal, metaplasia, gastric
- GSE210993 RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids 103 samples shares intestinal, metaplasia
- GSE291080 Clonal cell states link gastroesophageal junction tissues, metaplasia, and cancer [scRNA-seq] 45 samples shares metaplasia, scrna-seq
- GSE275145 Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Human scRNA-seq] 29 samples shares intestinal, scrna-seq
- GSE279915 Complexity of synovial fluid-derived monocyte–macrophage lineage cells in knee osteoarthritis 12 samples shares complexity, lineage
- GSE49711 RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq] 498 samples shares complexity
- GSE288179 Differential response of patient-derived intestinal organoids to site-specific mucosal bacteria in pediatric inflammatory bowel disease 105 samples shares intestinal
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.