A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D
Summary: 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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723002836 |
| _version_ | 1797824490218979328 |
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| author | Mathilde Bouchet Séverine Urdy Wenyue Guan Chérif Kabir Steve Garvis Jonathan Enriquez |
| author_facet | Mathilde Bouchet Séverine Urdy Wenyue Guan Chérif Kabir Steve Garvis Jonathan Enriquez |
| author_sort | Mathilde Bouchet |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-13T10:39:46Z |
| format | Article |
| id | doaj.art-1c024d7222754de29581786e2954d439 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-13T10:39:46Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-1c024d7222754de29581786e2954d4392023-05-18T04:40:16ZengElsevierSTAR Protocols2666-16672023-06-0142102316A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3DMathilde Bouchet0Séverine Urdy1Wenyue Guan2Chérif Kabir3Steve Garvis4Jonathan Enriquez5Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon, CNRS, University Lyon 1, 46 Allée d’Italie Cedex 07, 69364 Lyon, France; Corresponding authorInstitut de Génomique Fonctionnelle de Lyon, ENS de Lyon, CNRS, University Lyon 1, 46 Allée d’Italie Cedex 07, 69364 Lyon, FranceInstitut de Génomique Fonctionnelle de Lyon, ENS de Lyon, CNRS, University Lyon 1, 46 Allée d’Italie Cedex 07, 69364 Lyon, FranceInstitut de Génomique Fonctionnelle de Lyon, ENS de Lyon, CNRS, University Lyon 1, 46 Allée d’Italie Cedex 07, 69364 Lyon, FranceLaboratoire de Biologie Moléculaire de la Cellule ENS de Lyon, CNRS, University Lyon 1, HCL, 46 Allée d'Italie cedex 07, 69364 Lyon, FranceInstitut de Génomique Fonctionnelle de Lyon, ENS de Lyon, CNRS, University Lyon 1, 46 Allée d’Italie Cedex 07, 69364 Lyon, France; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723002836BioinformaticsCell BiologyDevelopmental biologyMicroscopyMolecular BiologyIn Situ Hybridization |
| spellingShingle | Mathilde Bouchet Séverine Urdy Wenyue Guan Chérif Kabir Steve Garvis Jonathan Enriquez A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D STAR Protocols Bioinformatics Cell Biology Developmental biology Microscopy Molecular Biology In Situ Hybridization |
| 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 | Bioinformatics Cell Biology Developmental biology Microscopy Molecular Biology In Situ Hybridization |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723002836 |
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