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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
要旨

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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製品内容

Sigma-Aldrich
アセトン, ACS reagent, ≥99.5%
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ジメチルスルホキシド, ACS reagent, ≥99.9%
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塩化ナトリウム, ACS reagent, ≥99.0%
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ペプシン ブタ胃粘膜由来, powder, ≥250 units/mg solid
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ホルムアルデヒド 溶液, for molecular biology, 36.5-38% in H2O
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塩化マグネシウム, anhydrous, ≥98%
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ドデシル硫酸ナトリウム 溶液, BioUltra, for molecular biology, 10% in H2O
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SSC バッファー 20×濃縮液, for Northern and Southern blotting, solution
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ベタイン, BioUltra, ≥99.0% (NT)
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アクチノマイシンD, from Streptomyces sp., ~98% (HPLC)
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トリズマ® 塩基, BioXtra, pH 10.5-12.0 (1 M in H2O), ≥99.9% (titration)
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N-ラウロイルサルコシン ナトリウム塩 溶液, 30% aqueous solution, ≥97.0% (HPLC)
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Eosin Y Solution, Aqueous
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トリズマ® 塩酸塩 塩酸塩, BioXtra, pH 3.5-5.0 (0.5 M in H2O), ≥99.0% (titration)
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