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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: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10475847/ https://www.ncbi.nlm.nih.gov/pubmed/37671011 http://dx.doi.org/10.1016/j.crmeth.2023.100548 |
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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 sequencing (RNA-seq) multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10× 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 6 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-10475847 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-104758472023-09-05 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. Cell Rep Methods Report 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 sequencing (RNA-seq) multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10× 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 6 weeks later. Our data show sci-Plex’s potential to dramatically scale up the analysis of treatment conditions on relevant human models. Elsevier 2023-08-09 /pmc/articles/PMC10475847/ /pubmed/37671011 http://dx.doi.org/10.1016/j.crmeth.2023.100548 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Report 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 | Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10475847/ https://www.ncbi.nlm.nih.gov/pubmed/37671011 http://dx.doi.org/10.1016/j.crmeth.2023.100548 |
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