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

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

Communications biology (2021-01-10)
Linda Kvastad, Konstantin Carlberg, Ludvig Larsson, Eva Gracia Villacampa, Alexander Stuckey, Linnea Stenbeck, Annelie Mollbrink, Margherita Zamboni, Jens Peter Magnusson, Elisa Basmaci, Alia Shamikh, Gabriela Prochazka, Anna-Lena Schaupp, Åke Borg, Lars Fugger, Monica Nistér, Joakim Lundeberg
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 demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows.

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