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Changes of transcript switch usage induced by TGF-b signaling in the in vitro decidualization

GSE261366 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2025/08/06 Platform GPL26167Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 21 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
21 samples: 7 conditions, mostly in triplicateGroups 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 systems-based approach to uterine fibroids identifies differential splicing associated with abnormal uterine bleedingCommunications medicine · 2025
Summary (written by the submitters)
To probe potential switches in transcript usage induced by TGF-beta signalling within endometrium, we treated the THESC (hTERT-immortalized Human Endometrial Stromal Cells) cell line with TGF-beta during in vitro decidualization and monitored transcript-level changes using Nanopore long-read sequencing allowing unambiguous determination of transcript isoforms.
Published in
A systems-based approach to uterine fibroids identifies differential splicing associated with abnormal uterine bleeding
Wang CY, Philpott M, P O'Brien D et al. · Communications medicine 2025 · PMID 40739398 · doi:10.1038/s43856-025-01051-x
This dataset
Open GSE261366 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 GSE261366_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 PRJNA1086567 and SRA study SRP494634. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40739398) ↗
Study design
7 conditions, mostly in triplicate
THESC, no hormone induction, Day0, biol ×3 THESC, hormone induced decidualization, Day3, ×3 THESC, no hormone induction, Ctrl, Day0, biol ×3 THESC, hormone induced decidualization, DMSO,… ×3 THESC, hormone induced decidualization, TGF-b… ×3 THESC, hormone induced decidualization, TGF-b… ×3 THESC, hormone induced decidualization, MEK i… ×3

Supports a case/control comparison: 12 samples read as cases, 3 as controls.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 of them. 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

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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.