An organoid model of the menstrual cycle reveals the role of the luminal epithelium in regeneration of the human endometrium

Analysis code

Authors

Affiliations

Konstantina Nikolakopoulou

Friedrich Miescher Institute for Biomedical Research

Weand Ybañez

Friedrich Miescher Institute for Biomedical Research

Lhéanna Klaeylé

Friedrich Miescher Institute for Biomedical Research

Lisa Frugoli

Friedrich Miescher Institute for Biomedical Research

Hans-Rudolf Hotz

Friedrich Miescher Institute for Biomedical Research

SIB Swiss Institute of Bioinformatics

Charlotte Soneson

Friedrich Miescher Institute for Biomedical Research

SIB Swiss Institute of Bioinformatics

Margherita Yayoi Turco

Friedrich Miescher Institute for Biomedical Research

Links to publication

The accompanying manuscript is:

Nikolakopoulou et al.: An organoid model of the menstrual cycle reveals the role of the luminal epithelium in regeneration of the human endometrium (2025)

which is available from:

• bioRxiv

Links to analysis code

All source code is available from GitHub at https://github.com/fmicompbio/IVMC-protocol. Click on a thumbnail below to jump directly to the corresponding sources.

Bulk RNA-seq

Data processing, analysis and plotting Supplementary Tables
Deconvolution, processing
Deconvolution, paper figures

scRNA-seq, epithelial atlas

Data processing Supplementary Tables, marker genes Supplementary Tables, GO term enrichments
Paper figures

scRNA-seq, timecourse

Data processing Supplementary Tables, marker genes Supplementary Tables, GO term enrichments
Paper figures

scRNA-seq, complete atlas (CellChat analysis)

Data processing
CellChat analysis
Paper figures