The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
(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.
(Less)
- author
- organization
- publishing date
- 2021
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Communications Biology
- volume
- 4
- issue
- 1
- article number
- 57
- publisher
- Nature Publishing Group
- external identifiers
-
- pmid:33420318
- scopus:85098933855
- 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
- 2024-09-19 14:52:00
@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}}, }