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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...

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Autores principales: Tresenrider, Amy, Sridhar, Akshayalakshmi, Eldred, Kiara C., Cuschieri, Sophia, Hoffer, Dawn, Trapnell, Cole, Reh, Thomas A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
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.
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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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