The spatial RNA integrity number assay for in situ evaluation of transcriptome quality

The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have e...

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Autores principales: Kvastad, Linda, Carlberg, Konstantin, Larsson, Ludvig, Villacampa, Eva Gracia, Stuckey, Alexander, Stenbeck, Linnea, Mollbrink, Annelie, Zamboni, Margherita, Magnusson, Jens Peter, Basmaci, Elisa, Shamikh, Alia, Prochazka, Gabriela, Schaupp, Anna-Lena, Borg, Åke, Fugger, Lars, Nistér, Monica, Lundeberg, Joakim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7794352/
https://www.ncbi.nlm.nih.gov/pubmed/33420318
http://dx.doi.org/10.1038/s42003-020-01573-1
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author Kvastad, Linda
Carlberg, Konstantin
Larsson, Ludvig
Villacampa, Eva Gracia
Stuckey, Alexander
Stenbeck, Linnea
Mollbrink, Annelie
Zamboni, Margherita
Magnusson, Jens Peter
Basmaci, Elisa
Shamikh, Alia
Prochazka, Gabriela
Schaupp, Anna-Lena
Borg, Åke
Fugger, Lars
Nistér, Monica
Lundeberg, Joakim
author_facet Kvastad, Linda
Carlberg, Konstantin
Larsson, Ludvig
Villacampa, Eva Gracia
Stuckey, Alexander
Stenbeck, Linnea
Mollbrink, Annelie
Zamboni, Margherita
Magnusson, Jens Peter
Basmaci, Elisa
Shamikh, Alia
Prochazka, Gabriela
Schaupp, Anna-Lena
Borg, Åke
Fugger, Lars
Nistér, Monica
Lundeberg, Joakim
author_sort Kvastad, Linda
collection PubMed
description The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have emerged and shown their value by placing gene expression into a tissue context, resulting in transcriptional information from all tissue regions. Thus, the ability to estimate RNA quality in situ has become of utmost importance to overcome the limitation with a bulk rRNA measurement. Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows.
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spelling pubmed-77943522021-01-15 The spatial RNA integrity number assay for in situ evaluation of transcriptome quality Kvastad, Linda Carlberg, Konstantin Larsson, Ludvig Villacampa, Eva Gracia Stuckey, Alexander Stenbeck, Linnea Mollbrink, Annelie Zamboni, Margherita Magnusson, Jens Peter Basmaci, Elisa Shamikh, Alia Prochazka, Gabriela Schaupp, Anna-Lena Borg, Åke Fugger, Lars Nistér, Monica Lundeberg, Joakim Commun Biol Article The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have emerged and shown their value by placing gene expression into a tissue context, resulting in transcriptional information from all tissue regions. Thus, the ability to estimate RNA quality in situ has become of utmost importance to overcome the limitation with a bulk rRNA measurement. Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows. Nature Publishing Group UK 2021-01-08 /pmc/articles/PMC7794352/ /pubmed/33420318 http://dx.doi.org/10.1038/s42003-020-01573-1 Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Kvastad, Linda
Carlberg, Konstantin
Larsson, Ludvig
Villacampa, Eva Gracia
Stuckey, Alexander
Stenbeck, Linnea
Mollbrink, Annelie
Zamboni, Margherita
Magnusson, Jens Peter
Basmaci, Elisa
Shamikh, Alia
Prochazka, Gabriela
Schaupp, Anna-Lena
Borg, Åke
Fugger, Lars
Nistér, Monica
Lundeberg, Joakim
The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
title The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
title_full The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
title_fullStr The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
title_full_unstemmed The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
title_short The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
title_sort spatial rna integrity number assay for in situ evaluation of transcriptome quality
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7794352/
https://www.ncbi.nlm.nih.gov/pubmed/33420318
http://dx.doi.org/10.1038/s42003-020-01573-1
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