Xenotransplanted Human Small Intestinal Organoids Reveal the Transepithelial Zinc Transport Pathway as a Key Mediator of Intestinal Adaptation in Short Bowel Syndrome
Single-cell RNA-seq · human · 11 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 11 samples: 11 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
- Xenotransplanted human organoids identify transepithelial zinc transport as a key mediator of intestinal adaptationNature communications · 2024
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 GSE271065_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1129535 and SRA study SRP516845. 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 11 sample titles: 11 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.
- GSM8368051 SBS replicate 1, human organoid
- GSM8368052 SBS replicate 2, human organoid
- GSM8368053 SBS replicate 3, human organoid
- GSM8368054 SBS replicate 4, human organoid
- GSM8368055 SBS replicate 5, human organoid
- GSM8368056 SHAM replicate 1, human organoid
- GSM8368057 SHAM replicate 2, human organoid
- GSM8368058 SHAM replicate 3-1, human organoid
- GSM8368059 SHAM replicate 3-2, human organoid
- GSM8368060 SHAM replicate 4, human organoid
- GSM8368061 SHAM replicate 5, human organoid
- GSE210993 RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids 103 samples shares intestinal, organoids
- GSE320151 Transcriptomic profiling reveals substrate- and shear stress_x0002_dependent maturation of human small intestinal epithelial cells 58 samples shares intestinal, small
- GSE297090 Distinct Molecular Responses of Human Intestinal Organoids to Proton and Photon Radiation 40 samples shares intestinal, organoids
- GSE210991 5' droplet-based single cell RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids [scRNA-seq] 29 samples shares intestinal, organoids
- GSE298715 Primary human intestinal organoids recapitulate enteric infection of monkeypox virus and enable scalable drug discovery 18 samples shares intestinal, organoids
- GSE309917 Inducible POU2F3 expression in human intestinal organoids as a model of human tuft cells 12 samples shares intestinal, organoids
- GSE230718 Generation of intestinal organoids from human urine cells 12 samples shares intestinal, organoids
- 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.