Elements of sample preparation and reagent quality control in spatial transcriptome experiments

Overall flow and key nodes of spatial transcriptome experiments

Spatial transcriptome technology aims to obtain RNA expression and spatial coordinate information in situ in tissue sections.Common processes generally include tissue sampling and freezing, Oct embedding, frozen sectioning, tissue patching, fixation and permeability, in-situ capture or chip hybridization, cDNA synthesis, library construction and high-throughput sequencing, and subsequent data analysis.Each node may affect the integrity of spatial information, so reagent and consumable material quality control needs to be carried out throughout the process.

It should be emphasized that the spatial transcriptome is currently mainly used as a tool for life science research, and related reagents and instruments should be managed according to scientific research purposes.When establishing the method, the laboratory should pre-test the key steps in conjunction with its own sample type, rather than directly copying the default conditions of a platform.

Precautions for organizing the preservation and slicing process

Tissue RNA integrity has a greater impact on spatial transcriptome results.A common practice is to quickly freeze liquid nitrogen or use a special tissue preservative solution as soon as possible after sampling to reduce RNA degradation.For paraffin-embedded samples, it is generally necessary to evaluate the degree of RNA fragmentation and select a spatial transcriptome protocol suitable for the paraffin sample.The thickness of frozen sections is often between a few microns and a dozen microns. Different tissue types need to explore the appropriate thickness to ensure that the tissue morphology is complete and the chip capture efficiency is acceptable.

Clean RNase-free cryotubes, blades and slides should be prepared in advance before sampling.

Slicing Environment Recommended Control of Humidity and Temperature