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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 and Basmaci, Elisa , et al. (2021) In Communications Biology 4(1).
Abstract

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... (More)

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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publishing date
type
Contribution to journal
publication status
published
subject
in
Communications Biology
volume
4
issue
1
article number
57
publisher
Nature Publishing Group
external identifiers
  • scopus:85098933855
  • pmid:33420318
ISSN
2399-3642
DOI
10.1038/s42003-020-01573-1
language
English
LU publication?
yes
id
c7a6cfde-2d96-4991-b4ec-9b5a9286b81c
date added to LUP
2021-01-19 08:34:35
date last changed
2024-06-13 05:35:35
@article{c7a6cfde-2d96-4991-b4ec-9b5a9286b81c,
  abstract     = {{<p>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.</p>}},
  author       = {{Kvastad, Linda and Carlberg, Konstantin and Larsson, Ludvig and Villacampa, Eva Gracia and Stuckey, Alexander and Stenbeck, Linnea and Mollbrink, Annelie and Zamboni, Margherita and Magnusson, Jens Peter and Basmaci, Elisa and Shamikh, Alia and Prochazka, Gabriela and Schaupp, Anna Lena and Borg, Åke and Fugger, Lars and Nistér, Monica and Lundeberg, Joakim}},
  issn         = {{2399-3642}},
  language     = {{eng}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Communications Biology}},
  title        = {{The spatial RNA integrity number assay for in situ evaluation of transcriptome quality}},
  url          = {{http://dx.doi.org/10.1038/s42003-020-01573-1}},
  doi          = {{10.1038/s42003-020-01573-1}},
  volume       = {{4}},
  year         = {{2021}},
}