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---
title: "An organoid model of the menstrual cycle reveals the role of the luminal epithelium in regeneration of the human endometrium"
subtitle: "Analysis code"
date: ""
author:
- name: Konstantina Nikolakopoulou
orcid: 0000-0003-2306-590X
email: konstantina.nikolakopoulou@fmi.ch
affiliations:
- ref: fmi
- name: Weand Ybañez
orcid: 0009-0004-9494-819X
email:
affiliations:
- ref: fmi
- name: Lhéanna Klaeylé
orcid: 0009-0001-3774-2767
email:
affiliations:
- ref: fmi
- name: Lisa Frugoli
orcid: 0009-0009-2997-1197
email:
affiliations:
- ref: fmi
- name: Tereza Cindrova-Davies
email:
affiliations:
- ref: cambridge
- name: Hans-Rudolf Hotz
orcid: 0000-0002-2799-424X
email: hansrudolf.hotz@fmi.ch
affiliations:
- ref: fmi
- ref: sib
- name: Charlotte Soneson
orcid: 0000-0003-3833-2169
email: charlotte.soneson@fmi.ch
affiliations:
- ref: fmi
- ref: sib
- name: Margherita Yayoi Turco
orcid: 0000-0002-3380-7375
email: margherita.turco@fmi.ch
affiliations:
- ref: fmi
affiliations:
- id: fmi
name: Friedrich Miescher Institute for Biomedical Research
address: Fabrikstrasse 24
postal-code: 4056
city: Basel
country: Switzerland
- id: unibas
name: University of Basel
address: Petersplatz 10
postal-code: 4003
city: Basel
country: Switzerland
- id: sib
name: SIB Swiss Institute of Bioinformatics
address: Fabrikstrasse 24
postal-code: 4056
city: Basel
country: Switzerland
- id: cambridge
name: Loke Centre for Trophoblast Research, University of Cambridge
city: Cambridge
country: United Kingdom
license: MIT License
format:
html:
embed-resources: true
fig-cap-location: top
---
<style>
.author {
font-size: 1em;
}
.affiliation {
font-size: 1em;
}
</style>
## Links to publication
The accompanying manuscript is:
Nikolakopoulou et al.: An in vitro menstrual cycle using organoids captures epithelial cell transitions during menstruation and regeneration of the human endometrium. Cell Stem Cell 33(5):747-762.e8 (2026)
which is available from:
- [Cell Stem Cell](https://doi.org/10.1016/j.stem.2026.04.005)
- [bioRxiv](https://doi.org/10.1101/2025.07.03.663000)
## Links to data
* Bulk RNA-seq raw data: [E-MTAB-15118](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15118)
* Single-cell RNA-seq raw data: [E-MTAB-15330](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15330)
* Luminex raw data: [Mendeley Data](https://doi.org/10.17632/vpmzzd54r5.1)
* Processed single-cell data: [Zenodo](https://doi.org/10.5281/zenodo.22015161)
## Links to analysis code
All source code is available from GitHub at [https://github.com/fmicompbio/IVMC-protocol](https://github.com/fmicompbio/IVMC-protocol) and archived on [Zenodo](https://doi.org/10.5281/zenodo.19334152).
Click on a thumbnail below to jump directly to the corresponding sources.
### Bulk RNA-seq
| | |
|----------|:----------:|
| [Data processing, analysis and plotting](bulkRNAseq_timecourse/IVMC_analysis_and_plots_for_paper.html) <br> [Supplementary Tables](https://github.com/fmicompbio/IVMC-protocol/tree/main/bulkRNAseq_timecourse/paper_tables_IVMC/) | [{width="4cm"}](bulkRNAseq_timecourse/IVMC_analysis_and_plots_for_paper.html) |
| [Deconvolution, processing](bulkRNAseq_timecourse/deconvolve_bulk_timecourse.html) | |
| [Deconvolution, paper figures](bulkRNAseq_timecourse/deconvolution_figures_for_paper.html) | [{width="6cm"}](bulkRNAseq_timecourse/deconvolution_figures_for_paper.html) |
: {tbl-colwidths="[50,50]"}
### scRNA-seq, epithelial atlas
| | |
|----------|:----------:|
| [Data processing](scRNAseq_invivo_endometrium_epithelial_cell_atlas/process_epithelial_cell_atlas.html) <br> [Supplementary Tables, marker genes](https://github.com/fmicompbio/IVMC-protocol/tree/main/scRNAseq_invivo_endometrium_epithelial_cell_atlas/marker_genes_all_leiden_res0.4_annot) <br> [Supplementary Tables, GO term enrichments](https://github.com/fmicompbio/IVMC-protocol/tree/main/scRNAseq_invivo_endometrium_epithelial_cell_atlas/gprofiler) | |
| [Paper figures](scRNAseq_invivo_endometrium_epithelial_cell_atlas/epithelial_atlas_figures_for_paper.html) | [{width="4cm"}](scRNAseq_invivo_endometrium_epithelial_cell_atlas/epithelial_atlas_figures_for_paper.html) |
: {tbl-colwidths="[50,50]"}
### scRNA-seq, timecourse
| | |
|----------|:----------:|
| [Data processing](scRNAseq_timecourse/process_organoid_scrnaseq_timecourse.html) <br> [Supplementary Tables, marker genes](https://github.com/fmicompbio/IVMC-protocol/tree/main/) <br> [Supplementary Tables, GO term enrichments](https://github.com/fmicompbio/IVMC-protocol/tree/main/scRNAseq_timecourse/gprofiler) | |
| [Paper figures](scRNAseq_timecourse/scRNAseq_timecourse_figures_for_paper.html) | [{width="4cm"}](scRNAseq_timecourse/scRNAseq_timecourse_figures_for_paper.html) |
: {tbl-colwidths="[50,50]"}
### scRNA-seq, complete atlas (CellChat analysis)
| | |
|----------|:----------:|
| [Data processing](scRNAseq_invivo_endometrium_cell_atlas/process_cell_atlas.html) | |
| [CellChat analysis](scRNAseq_invivo_endometrium_cell_atlas/run_cellchat.html) | [{width="4cm"}](scRNAseq_invivo_endometrium_cell_atlas/run_cellchat.html) |
| [Paper figures](scRNAseq_invivo_endometrium_cell_atlas/cell_atlas_figures_for_paper.html) | [{width="4cm"}](scRNAseq_invivo_endometrium_cell_atlas/cell_atlas_figures_for_paper.html) |
: {tbl-colwidths="[50,50]"}