RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids
RNA-seq (gene expression) · human · 103 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
- 103 samples: 103 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
- Divergent lineage trajectories and genetic landscapes in human gastric intestinal metaplasia organoids associated with early neoplastic progressionGut · 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 GSE210993_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: 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 PRJNA868483. 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 103 sample titles: 103 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.
- GSM6443942 GX001-IM3O [RNA-seq]
- GSM6443943 GX006-IM3O [RNA-seq]
- GSM6443944 GX014-IM2O [RNA-seq]
- GSM6443945 GX023-IM2O [RNA-seq]
- GSM6443946 GX023-IM3dysO [RNA-seq]
- GSM6443947 GX031-IMO [RNA-seq]
- GSM6443948 GX040-IMO [RNA-seq]
- GSM6443949 GX049-IMO [RNA-seq]
- GSM6443950 GX054-IM2O [RNA-seq]
- GSM6443951 GX059-IMO-P15 [RNA-seq]
- GSM6443952 GX060-IMO [RNA-seq]
- GSM6443953 GX062-IM2O [RNA-seq]
- GSM6443954 GX062-IMO [RNA-seq]
- GSM6443955 GX072-IM3O [RNA-seq]
- GSM6443956 GX072-IMO [RNA-seq]
- GSM6443957 GX076-IM2O [RNA-seq]
- GSM6443958 GX076-IMO [RNA-seq]
- GSM6443959 GX078-IM2O [RNA-seq]
- GSM6443960 GX085-IMO [RNA-seq]
- GSM6443961 GX088-IMO [RNA-seq]
- GSM6443962 GX091-AgO [RNA-seq]
- GSM6443963 GX091-BlO [RNA-seq]
- GSM6443964 GX092-BO [RNA-seq]
- GSM6443965 GX094-IMO [RNA-seq]
- GSM6443966 GX098-IMO [RNA-seq]
- GSM6443967 GX099-IM2O [RNA-seq]
- GSM6443968 GX099-IMO [RNA-seq]
- GSM6443969 GX001-IM3O_P30 [RNA-seq]
- GSM6443970 GX059-IMOL [RNA-seq]
- GSM6443971 GX072-IM3OL [RNA-seq]
- GSM6443972 GX072-IMOL [RNA-seq]
- GSM6443973 GX076-IMOL [RNA-seq]
- GSM6443974 GX058-AO [RNA-seq]
- GSM6443975 GX072-AO [RNA-seq]
- GSM6443976 GX080-IMO [RNA-seq]
- GSM6443977 GX082-AO [RNA-seq]
- GSM6443978 GX086-IM2O [RNA-seq]
- GSM6443979 GX087-IM2O [RNA-seq]
- GSM6443980 GX089-AgO [RNA-seq]
- GSM6443981 GX089-AlO [RNA-seq]
+ 63 more — browse all 103 samples with per-sample file links →
- GSE210991 5' droplet-based single cell RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids [scRNA-seq] 29 samples shares gastrointestinal, intestinal, metaplasia, organoids
- GSE290695 Identification of Crohn’s disease subtypes in single cell RNA sequencing signatures of treatment naïve samples across the gastrointestinal tract 95 samples shares gastrointestinal, intestinal
- GSE308421 Single-Cell RNA Sequencing Analysis of Intestinal organoids expanded in either IntestiCult™ Plus or IntestiCult™ OGM (Human) 10 samples shares intestinal, organoids
- GSE301351 The single-cell transcriptome defines an effector Vd1 gd T cell-dependent anti-tumor immunity in human gastrointestinal stromal tumor (GIST) [10X] 6 samples shares gastrointestinal, intestinal
- GSE295401 Spatial transcriptomics reveal lineage complexity of gastric incomplete intestinal metaplasia and its association with gastric cancers [scRNA-Seq] 10 samples shares intestinal, metaplasia
- GSE210995 HKU Gastric Intestinal Metaplasia study: Single-cell RNA sequencing, transcriptome and methylation profiling 199 samples shares intestinal, metaplasia
- GSE313894 Single cell characterization of the gastrointestinal HIV reservoir reveals heterogeneous cellular phenotypes. 68 samples shares gastrointestinal, intestinal
- GSE241924 Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (ChIP-Seq) 45 samples shares gastrointestinal, 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.