← BioTransfer GEO Dataset Finder
GEO series

In vitro generation of a ureteral organoid from pluripotent stem cells

GSE282077 Homo sapiens (human) RNA-seq (gene expression) 11 samples Submitted 2025/06/24 Platform GPL20795Platform GPL21273
At a glance

RNA-seq (gene expression) · human · 11 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
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
In vitro generation of a ureteral organoid from pluripotent stem cellsNature communications · 2025
Summary (written by the submitters)
The ureter is the outlet for urine produced by the kidney. Recent advances in stem cell biology have enabled the in vitro generation of kidney organoids from pluripotent stem cells (PSCs), but they lack the ureter, which hinders the smooth drainage of urine. By mimicking the in vivo developmental process of ureteral stromal progenitors (SPs) from the posterior intermediate mesoderm, we report here in vitro induction protocols for ureteral SPs from mouse and human PSCs.
Read the full summary ↓
When the induced SPs were combined with ureteral epithelia derived from mouse embryos, the elongated, multilayered ureteral structure was reconstituted, exhibiting peristaltic constriction. The ureter-like spherical organoids entirely derived from mouse PSCs can also be generated by combining the induced SPs and the epithelial progenitor, the ureteric bud. Furthermore, ureteral SPs induced from TBX18-deficient human PSCs recapitulate the disease state of a congenital anomaly of the urinary tract. Therefore, our induction protocols for ureteral SPs will be useful for the elucidation of ureteral development and disease, and will be an important step towards functional kidney organoids with urine flow.
Published in
In vitro generation of a ureteral organoid from pluripotent stem cells
Ibi Y, Miike K, Ohmori T et al. · Nature communications 2025 · PMID 40541956 · doi:10.1038/s41467-025-60693-6
This dataset
Open GSE282077 in finder → Find more 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 GSE282077_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 PRJNA1186954 and SRA study SRP545605. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40541956) ↗
Study design
11 samples, each with a distinct title — no replicated groups

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.

Samples in this study
Datasets on a similar topic

Search all 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.