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Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity
With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312535/ https://www.ncbi.nlm.nih.gov/pubmed/37398481 http://dx.doi.org/10.1101/2023.05.31.543087 |
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author | Tresenrider, Amy Sridhar, Akshayalakshmi Eldred, Kiara C. Cuschieri, Sophia Hoffer, Dawn Trapnell, Cole Reh, Thomas A. |
author_facet | Tresenrider, Amy Sridhar, Akshayalakshmi Eldred, Kiara C. Cuschieri, Sophia Hoffer, Dawn Trapnell, Cole Reh, Thomas A. |
author_sort | Tresenrider, Amy |
collection | PubMed |
description | With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA-seq multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10x methods produce highly concordant cell class compositions and then expand sci-Plex to analyze the cell class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to six weeks later. Our data show sci-Plex’s potential to dramatically scale-up the analysis of treatment conditions on relevant human models. |
format | Online Article Text |
id | pubmed-10312535 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-103125352023-07-01 Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity Tresenrider, Amy Sridhar, Akshayalakshmi Eldred, Kiara C. Cuschieri, Sophia Hoffer, Dawn Trapnell, Cole Reh, Thomas A. bioRxiv Article With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA-seq multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10x methods produce highly concordant cell class compositions and then expand sci-Plex to analyze the cell class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to six weeks later. Our data show sci-Plex’s potential to dramatically scale-up the analysis of treatment conditions on relevant human models. Cold Spring Harbor Laboratory 2023-06-03 /pmc/articles/PMC10312535/ /pubmed/37398481 http://dx.doi.org/10.1101/2023.05.31.543087 Text en https://creativecommons.org/licenses/by-nc/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (https://creativecommons.org/licenses/by-nc/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator. |
spellingShingle | Article Tresenrider, Amy Sridhar, Akshayalakshmi Eldred, Kiara C. Cuschieri, Sophia Hoffer, Dawn Trapnell, Cole Reh, Thomas A. Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity |
title | Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity |
title_full | Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity |
title_fullStr | Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity |
title_full_unstemmed | Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity |
title_short | Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity |
title_sort | single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312535/ https://www.ncbi.nlm.nih.gov/pubmed/37398481 http://dx.doi.org/10.1101/2023.05.31.543087 |
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