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Tissue processing and RNA quality control

Open-ST requires the use of unfixed fresh-frozen tissue. We recommend following 10X Visium's protocol for simultaneous freezing and embedding in their Tissue Preparation guide.

Test for RNA quality of the OCT-embedded tissue before working with a tissue. For this we recommend cutting 5-10 sections of tissue at 10 um thickness. Remove excess OCT as possible and collect the tissue sections in a pre-cooled 1.5 mL tube. Extract total RNA and assess the RNA quality on an automated gel electrophoresis machine, such as the BioAnalyzer or TapeStation.

Aim for an RNA integrity number (RIN) over 7. Samples with lower RIN values can be used for Open-ST; however, low RNA integrity negatively impacts library quality.