A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D

Techniques allowing the precise quantification of mRNA at the cellular level are essential for understanding biological processes. Here, we present a semi-automated smiFISH (single-molecule inexpensive FISH) pipeline enabling quantification of mRNA in a small number of cells (∼40) in fixed whole mou...

Descripción completa

Detalles Bibliográficos
Autores principales: Bouchet, Mathilde, Urdy, Séverine, Guan, Wenyue, Kabir, Chérif, Garvis, Steve, Enriquez, Jonathan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10206206/
https://www.ncbi.nlm.nih.gov/pubmed/37195867
http://dx.doi.org/10.1016/j.xpro.2023.102316
_version_ 1785046176919191552
author Bouchet, Mathilde
Urdy, Séverine
Guan, Wenyue
Kabir, Chérif
Garvis, Steve
Enriquez, Jonathan
author_facet Bouchet, Mathilde
Urdy, Séverine
Guan, Wenyue
Kabir, Chérif
Garvis, Steve
Enriquez, Jonathan
author_sort Bouchet, Mathilde
collection PubMed
description Techniques allowing the precise quantification of mRNA at the cellular level are essential for understanding biological processes. Here, we present a semi-automated smiFISH (single-molecule inexpensive FISH) pipeline enabling quantification of mRNA in a small number of cells (∼40) in fixed whole mount tissue. We describe steps for sample preparation, hybridization, image acquisition, cell segmentation, and mRNA quantification. Although the protocol was developed in Drosophila, it can be optimized for use in other organisms. For complete details on the use and execution of this protocol, please refer to Guan et al.(1)
format Online
Article
Text
id pubmed-10206206
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Elsevier
record_format MEDLINE/PubMed
spelling pubmed-102062062023-05-25 A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D Bouchet, Mathilde Urdy, Séverine Guan, Wenyue Kabir, Chérif Garvis, Steve Enriquez, Jonathan STAR Protoc Protocol Techniques allowing the precise quantification of mRNA at the cellular level are essential for understanding biological processes. Here, we present a semi-automated smiFISH (single-molecule inexpensive FISH) pipeline enabling quantification of mRNA in a small number of cells (∼40) in fixed whole mount tissue. We describe steps for sample preparation, hybridization, image acquisition, cell segmentation, and mRNA quantification. Although the protocol was developed in Drosophila, it can be optimized for use in other organisms. For complete details on the use and execution of this protocol, please refer to Guan et al.(1) Elsevier 2023-05-16 /pmc/articles/PMC10206206/ /pubmed/37195867 http://dx.doi.org/10.1016/j.xpro.2023.102316 Text en © 2023 The Author(s) 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 Protocol
Bouchet, Mathilde
Urdy, Séverine
Guan, Wenyue
Kabir, Chérif
Garvis, Steve
Enriquez, Jonathan
A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D
title A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D
title_full A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D
title_fullStr A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D
title_full_unstemmed A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D
title_short A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D
title_sort simple smifish pipeline to quantify mrna at the single-cell level in 3d
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10206206/
https://www.ncbi.nlm.nih.gov/pubmed/37195867
http://dx.doi.org/10.1016/j.xpro.2023.102316
work_keys_str_mv AT bouchetmathilde asimplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT urdyseverine asimplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT guanwenyue asimplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT kabircherif asimplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT garvissteve asimplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT enriquezjonathan asimplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT bouchetmathilde simplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT urdyseverine simplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT guanwenyue simplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT kabircherif simplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT garvissteve simplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d
AT enriquezjonathan simplesmifishpipelinetoquantifymrnaatthesinglecelllevelin3d

Ejemplares similares