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 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. Researchers from Royal Institute of Technology (KTH) have developed a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. The researchers demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows.

The spatial RNA Integrity Number (sRIN) assay

Fig. 1

a Schematics of an one cell layer thick tissue section placed on a pre-printed fully coated capture area for 18S rRNA, leading to the formation of a c18RNA-footprint. b Schematic depiction of the sequential probe hybridization. c Total RNA gel electropherogram of a mouse olfactory bulb tissue sample together with d a heat map visualization of the section’s spatial RNA integrity number (sRIN) distribution based on its c18RNA footprint (n = 4, technical replicates) and e a HE image of the same section (scale bar: 600 µm), boxes enclose regions shown in close-up. f Close-up of HE image (scale bar: 200 µm) and g sRIN heat map, arrows marks cells from different areas in the tissue with high sRIN values, the left box depicts a group of cells where cell drop-out has occurred compared to the right box that depicts a group of cells recording high sRIN values.

Kvastad L, Carlberg K, Larsson L, Villacampa EG, Stuckey A, Stenbeck L, Mollbrink A, Zamboni M, Magnusson JP, Basmaci E, Shamikh A, Prochazka G, Schaupp AL, Borg Å, Fugger L, Nistér M, Lundeberg J. (2021) The spatial RNA integrity number assay for in situ evaluation of transcriptome quality. Commun Biol 4(1):57. [article]

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