Primary human intestinal organoids recapitulate enteric infection of monkeypox virus and enable scalable drug discovery
RNA-seq (gene expression) · human · 18 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
- 18 samples: 18 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
- Primary human intestinal organoids model enteric infection of monkeypox virus and enable scalable drug discoveryScience advances · 2026
Read the full summary ↓
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 GSE298715_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 PRJNA1270997 and SRA study SRP589441. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 15 samples read as cases, 3 as controls.
How we read this: Read from 18 sample titles: 18 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.
- GSM9021370 CTR1, Human intestinal organoids (healthy control, without infection)
- GSM9021371 CTR2, Human intestinal organoids (healthy control, without infection)
- GSM9021372 CTR3, Human intestinal organoids (healthy control, without infection)
- GSM9021373 CLO1, Human intestinal organoids infected with monkeypox virus, and treated with 1uM clofarabine for 96 hours
- GSM9021374 CLO2, Human intestinal organoids infected with monkeypox virus, and treated with 1uM clofarabine for 96 hours
- GSM9021375 CLO3, Human intestinal organoids infected with monkeypox virus, and treated with 1uM clofarabine for 96 hours
- GSM9021376 MP1A, Monkeypox virus infected intestinal organoids: samples harvested at 1 hour-post infection
- GSM9021377 MP1B, Monkeypox virus infected intestinal organoids: samples harvested at 1 hour-post infection
- GSM9021378 MP1C, Monkeypox virus infected intestinal organoids: samples harvested at 1 hour-post infection
- GSM9021379 MP24A, Monkeypox virus infected intestinal organoids: samples harvested at 24 hour-post infection
- GSM9021380 MP24B, Monkeypox virus infected intestinal organoids: samples harvested at 24 hour-post infection
- GSM9021381 MP24C, Monkeypox virus infected intestinal organoids: samples harvested at 24 hour-post infection
- GSM9021382 MP48A, Monkeypox virus infected intestinal organoids: samples harvested at 48 hour-post infection
- GSM9021383 MP48B, Monkeypox virus infected intestinal organoids: samples harvested at 48 hour-post infection
- GSM9021384 MP48C, Monkeypox virus infected intestinal organoids: samples harvested at 48 hour-post infection
- GSM9021385 MP96A, Monkeypox virus infected intestinal organoids: samples harvested at 96 hour-post infection
- GSM9021386 MP96B, Monkeypox virus infected intestinal organoids: samples harvested at 96 hour-post infection
- GSM9021387 MP96C, Monkeypox virus infected intestinal organoids: samples harvested at 96 hour-post infection
- GSE210993 RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids 103 samples shares intestinal, organoids
- GSE228249 Transcriptome analysis of primary human hepatocytes-derived organoids [RNA-seq] 82 samples shares organoids, primary
- GSE221608 Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participants of CRC 52 samples shares intestinal, primary
- GSE210991 5' droplet-based single cell RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids [scRNA-seq] 29 samples shares intestinal, organoids
- GSE217649 Bulk RNA sequencing for gene expression profileing of primary liver sinusoidal endothelial cells and iPSC-derived hepatic endoderm, septum mesenchymal cells, endothelial cells, and liver bud organoids 26 samples shares organoids, primary
- GSE298576 Mass generation and long-term expansion of hepatocyte organoids from adult primary hepatocytes 24 samples shares organoids, primary
- GSE263425 Modeling the Blood-Brain Barrier Formation and Cerebral Cavernous Malformations in human PSCs- and primary tissue-derived organoids 12 samples shares organoids, primary
- GSE308421 Single-Cell RNA Sequencing Analysis of Intestinal organoids expanded in either IntestiCult™ Plus or IntestiCult™ OGM (Human) 10 samples shares intestinal, organoids
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.