Yeast Single-cell RNA-seq, Cell by Cell and Step by Step

Single-cell RNA-seq (scRNA-seq) has become an established method for uncovering the intrinsic complexity within populations. Even within seemingly homogenous populations of isogenic yeast cells, there is a high degree of heterogeneity that originates from a compact and pervasively transcribed genome...

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Detalles Bibliográficos
Autores: Nadal Ribelles, Mariona, Islam, Saiful, Wei, Wu, Latorre Domenech, Pablo, Nguyen, Michelle, Nadal Clanchet, Eulàlia de, Posas, Francesc, Steinmetz, Lars M.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/220565
Acceso en línea:https://hdl.handle.net/2445/220565
Access Level:acceso abierto
Palabra clave:Transcripció genètica
Llevats
Genetic transcription
Yeast
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spelling Yeast Single-cell RNA-seq, Cell by Cell and Step by StepNadal Ribelles, MarionaIslam, SaifulWei, WuLatorre Domenech, PabloNguyen, MichelleNadal Clanchet, Eulàlia dePosas, FrancescSteinmetz, Lars M.Transcripció genèticaLlevatsGenetic transcriptionYeastSingle-cell RNA-seq (scRNA-seq) has become an established method for uncovering the intrinsic complexity within populations. Even within seemingly homogenous populations of isogenic yeast cells, there is a high degree of heterogeneity that originates from a compact and pervasively transcribed genome. Research with microorganisms such as yeast represents a major challenge for single-cell transcriptomics, due to their small size, rigid cell wall, and low RNA content per cell. Because of these technical challenges, yeast-specific scRNA-seq methodologies have recently started to appear, each one of them relying on different cell-isolation and library-preparation methods. Consequently, each approach harbors unique strengths and weaknesses that need to be considered. We have recently developed a yeast single-cell RNA-seq protocol (yscRNA-seq), which is inexpensive, high-throughput and easy-to-implement, tailored to the unique needs of yeast. yscRNA-seq provides a unique platform that combines single-cell phenotyping via index sorting with the incorporation of unique molecule identifiers on transcripts that allows to digitally count the number of molecules in a strand- and isoform-specific manner. Here, we provide a detailed, step-by-step description of the experimental and computational steps of yscRNA-seq protocol. This protocol will ease the implementation of yscRNA-seq in other laboratories and provide guidelines for the development of novel technologies.Bio-protocol LLC2025202520192025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion22 p.application/pdfhttps://hdl.handle.net/2445/220565Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a:  https://doi.org/10.21769/BioProtoc.3359Bio Protoc, 2019, vol. 9, num. 17https://doi.org/10.21769/BioProtoc.3359(c) Nadal Ribelles, Mariona et al., 2019info:eu-repo/semantics/openAccessoai:recercat.cat:2445/2205652026-05-29T05:05:01Z
dc.title.none.fl_str_mv Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
title Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
spellingShingle Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
Nadal Ribelles, Mariona
Transcripció genètica
Llevats
Genetic transcription
Yeast
title_short Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
title_full Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
title_fullStr Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
title_full_unstemmed Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
title_sort Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
dc.creator.none.fl_str_mv Nadal Ribelles, Mariona
Islam, Saiful
Wei, Wu
Latorre Domenech, Pablo
Nguyen, Michelle
Nadal Clanchet, Eulàlia de
Posas, Francesc
Steinmetz, Lars M.
author Nadal Ribelles, Mariona
author_facet Nadal Ribelles, Mariona
Islam, Saiful
Wei, Wu
Latorre Domenech, Pablo
Nguyen, Michelle
Nadal Clanchet, Eulàlia de
Posas, Francesc
Steinmetz, Lars M.
author_role author
author2 Islam, Saiful
Wei, Wu
Latorre Domenech, Pablo
Nguyen, Michelle
Nadal Clanchet, Eulàlia de
Posas, Francesc
Steinmetz, Lars M.
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Transcripció genètica
Llevats
Genetic transcription
Yeast
topic Transcripció genètica
Llevats
Genetic transcription
Yeast
description Single-cell RNA-seq (scRNA-seq) has become an established method for uncovering the intrinsic complexity within populations. Even within seemingly homogenous populations of isogenic yeast cells, there is a high degree of heterogeneity that originates from a compact and pervasively transcribed genome. Research with microorganisms such as yeast represents a major challenge for single-cell transcriptomics, due to their small size, rigid cell wall, and low RNA content per cell. Because of these technical challenges, yeast-specific scRNA-seq methodologies have recently started to appear, each one of them relying on different cell-isolation and library-preparation methods. Consequently, each approach harbors unique strengths and weaknesses that need to be considered. We have recently developed a yeast single-cell RNA-seq protocol (yscRNA-seq), which is inexpensive, high-throughput and easy-to-implement, tailored to the unique needs of yeast. yscRNA-seq provides a unique platform that combines single-cell phenotyping via index sorting with the incorporation of unique molecule identifiers on transcripts that allows to digitally count the number of molecules in a strand- and isoform-specific manner. Here, we provide a detailed, step-by-step description of the experimental and computational steps of yscRNA-seq protocol. This protocol will ease the implementation of yscRNA-seq in other laboratories and provide guidelines for the development of novel technologies.
publishDate 2019
dc.date.none.fl_str_mv 2019
2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/220565
url https://hdl.handle.net/2445/220565
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a:  https://doi.org/10.21769/BioProtoc.3359
Bio Protoc, 2019, vol. 9, num. 17
https://doi.org/10.21769/BioProtoc.3359
dc.rights.none.fl_str_mv (c) Nadal Ribelles, Mariona et al., 2019
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) Nadal Ribelles, Mariona et al., 2019
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 22 p.
application/pdf
dc.publisher.none.fl_str_mv Bio-protocol LLC
publisher.none.fl_str_mv Bio-protocol LLC
dc.source.none.fl_str_mv Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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