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

Summary, in English

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.

• Author: 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
• Department/s: LUCC: Lund University Cancer Centre; Familial Breast Cancer
• Publishing year: 2021
• Language: English
• Publication/Series: Communications Biology
• Volume: 4
• Issue: 1
• Links: http://dx.doi.org/10.1038/s42003-020-01573-1
• Document type: Journal article
• Publisher: Nature Publishing Group
• Topic: Biochemistry and Molecular Biology; Cell and Molecular Biology
• Status: Published
• Research group: Familial Breast Cancer
• ISBN/ISSN/Other: ISSN: 2399-3642