The quality of RNA from experimental materials is a crucial factor in determining the success of spatial transcriptomics experiments. To obtain better spatial transcriptomics data, we added RNA quality testing of sectioned cryoembedded materials before the formal spatial experiment.
To reduce RNA degradation caused by embedding, it is necessary to perform the entire embedding process on ice and to limit the embedding time. Given the small size of the material and the need for operation under a stereomicroscope, the embedding time was controlled within 40 minutes as much as possible. Under the condition of ensuring that the RNA integrity (RIN) of the material itself is ≥8.5, tissue sections were collected from the cryoembedded blocks. RNA was extracted using a trace RNA extraction kit and its quality was tested using the Agilent 4200. The RIN value of the sectioned RNA was 9.4 (it is generally considered that RNA integrity is good when the RIN reaches 7.0 or above), indicating that the RNA quality of the embedded material is high and suitable for subsequent spatial experiments.