Cellular crosstalk mediated by TGF-β drives epithelial-mesenchymal transition in patient-derived multilineage biliary organoids
RNA-seq (gene expression) · human · 14 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
- 14 samples: 14 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
- Cellular crosstalk mediated by TGF-β drives epithelial-mesenchymal transition in patient-derived multi-compartment biliary organoidsNature communications · 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 GSE266169_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 PRJNA1106050 and SRA study SRP502366. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 7 samples read as cases, 7 as controls.
How we read this: Read from 14 sample titles: 14 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.
- GSM8213924 MBO, Day 14, Control No.1, bulk RNA-seq
- GSM8213925 MBO, Day 14, Control No.2, bulk RNA-seq
- GSM8213926 MBO, Day 14, Control No.3, bulk RNA-seq
- GSM8213927 MBO, Day 14, BA patient No.1, bulk RNA-seq
- GSM8213928 MBO, Day 14, BA patient No.2, bulk RNA-seq
- GSM8213929 MBO, Day 14, BA patient No.3, bulk RNA-seq
- GSM8218095 MBO, Day 14, Control No.1, scRNA-seq
- GSM8218096 MBO, Day 14, Control No.2, scRNA-seq
- GSM8218097 MBO, Day 14, Control No.3, scRNA-seq
- GSM8218098 MBO, Day 14, Control No.4, scRNA-seq
- GSM8218099 MBO, Day 14, BA patient No.1, scRNA-seq
- GSM8218100 MBO, Day 14, BA patient No.2, scRNA-seq
- GSM8218101 MBO, Day 14, BA patient No.3, scRNA-seq
- GSM8218102 MBO, Day 14, BA patient No.4, scRNA-seq
- GSE231781 Single-cell atlas of patient-derived cervical organoids uncovers epithelial immune heterogeneity and intercellular crosstalk during Chlamydia infection 14 samples shares patient-derived, crosstalk, organoids, cellular
- GSE290615 miRNA/mRNA analysis of Chlamydia trachomatis-infected endometrial biopsies indicate increased TGF-β pathways drive epithelial-mesenchymal transition and regulatory T cell differentiation 15 samples shares tgf, epithelial-mesenchymal, transition
- GSE298139 Therapy-resistance in AT/RT is driven by epithelial-mesenchymal transition, extracellular matrix changes, and enrichment of CD1A+ CD207+ dendritic cells [snRNA-seq] 16 samples shares epithelial-mesenchymal, transition, cellular
- GSE298140 Therapy-resistance in AT/RT is driven by epithelial-mesenchymal transition, extracellular matrix changes, and enrichment of CD1A+ CD207+ dendritic cells [RNA-seq_FFPE] 12 samples shares epithelial-mesenchymal, transition, cellular
- GSE287174 Patient-Derived Meningioma Organoids: A Reliable Model for Studying Human Tumor Pathophysiology 65 samples shares patient-derived, organoids
- GSE262110 Patient-derived response estimates from zero-passage organoids of luminal breast cancer 35 samples shares patient-derived, organoids
- GSE302327 HIF-1alpha activity affects stem cell fate in patient-derived ileum organoids 29 samples shares patient-derived, organoids
- GSE324866 1.Effects of L013 treatment on gene expression in KYSE150 and KYSE510 cells. 2. 5 Patient-derived organoids RNA-seq data 27 samples shares patient-derived, 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.