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Comparative transcriptomic profiling of human 3D endometrial stromal organoids under distinct decidualization stimuli

GSE325553 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2026/03/25 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 20 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
20 samples: 7 × human endometrial stromal organoid, co-culture, vs 5 × human endometrial stromal organoid, EPC, vs 4 × human endometrial stromal organoid, control, vs 4 × human endometrial stromal organoid, cAMP,Groups 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
Hormonal stimulation induces broader decidualization responses than cyclic adenosine monophosphate alone in 3D human endometrial organoids†Biology of reproduction · 2026
Summary (written by the submitters)
Endometrial stromal decidualization is a hormone-regulated process essential for establishing uterine receptivity and supporting embryo implantation. Three-dimensional (3D) endometrial organoid systems provide a physiologically relevant platform to study this process; however, how different stimulatory conditions influence decidualization responses in 3D culture remains incompletely characterized.
Read the full summary ↓
In this study, we generated 3D human endometrial stromal organoids and subjected them to four experimental conditions: vehicle control, cyclic adenosine monophosphate (cAMP) stimulation, combined estrogen–progesterone–cAMP (EPC) treatment, and co-culture with in vitro–grown follicles derived from mouse ovary. Organoids were cultured for 6 days under each condition, followed by bulk RNA sequencing. Principal component analysis (PCA) revealed clear separation between control and stimulated groups, with cAMP, EPC, and follicle co-culture conditions showing distinct but partially overlapping transcriptional profiles. Differential gene expression analysis identified both shared and condition-specific transcriptional changes across the four treatments. Pathway-level analysis using gene set variation analysis (GSVA) further demonstrated common decidualization-associated biological processes alongside stimulus-specific functional responses. This dataset provides a comprehensive resource for investigating how distinct biochemical and paracrine stimuli regulate decidualization in 3D endometrial organoid systems. It enables comparative analysis of canonical cAMP-driven responses, hormone-mediated signaling, and follicle-derived paracrine effects on endometrial stromal decidualization.
Published in
Hormonal stimulation induces broader decidualization responses than cyclic adenosine monophosphate alone in 3D human endometrial organoids†
Liu S, Zhang J, Zhan T et al. · Biology of reproduction 2026 · PMID 42246078 · doi:10.1093/biolre/ioag117
This dataset
Open GSE325553 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 GSE325553_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 PRJNA1440464 and SRA study SRP685472. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42246078) ↗
Study design
7 × human endometrial stromal organoid, co-culture, vs 5 × human endometrial stromal organoid, EPC, vs 4 × human endometrial stromal organoid, control, vs 4 × human endometrial stromal organoid, cAMP,

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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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