← BioTransfer GEO Dataset Finder
GEO series

A "living biobank" of Crohn's Disease

GSE192819 Homo sapiens (human) RNA-seq (gene expression) 54 samples Submitted 2024/03/31 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 54 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
54 samples: 43 distinct titles, 11 of them repeatedGroups 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
A living organoid biobank of patients with Crohn's disease reveals molecular subtypes for personalized therapeuticsCell reports. Medicine · 2024
Summary (written by the submitters)
Patient-derived organoids (PDOs) from the colons of patients with Crohn's Disease (or healthy controls) were subjected to in-depth genotype, transcriptome and phenotype assessment. These studies revealed that CD may be classified broadly into two molecular subtypes, each with its unique profile of dysregulated celluar processes. We further show that these phenotypes can be rectified with matched therapeutics, hence making such intervention personalized. Findings show that CD-PDOs could serve as pre-clinical platforms for drug discovery and personalized medicine.
Published in
A living organoid biobank of patients with Crohn's disease reveals molecular subtypes for personalized therapeutics
Tindle C, Fonseca AG, Taheri S et al. · Cell reports. Medicine 2024 · PMID 39332415 · doi:10.1016/j.xcrm.2024.101748
This dataset
Open GSE192819 in finder → Find more human RNA-seq datasets →
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 GSE192819_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 PRJNA793263 and SRA study SRP352959. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39332415) ↗
Study design
43 distinct titles, 11 of them repeated
CD23_LC_S ×2 CD61_LC_S ×2 CD68_LC_S ×2 CD69_LC_S ×2 CD74_LC_S ×2 H14_colon_S ×2 UC41_LC_S ×2 UC71_LC_S ×2 +3 more

How we read this: Read from 54 sample titles: 43 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.

Samples in this study

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

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.