Question: Can I perform both Single Cell Gene Expression and Visium Spatial Gene Expression experiments on my OCT-embedded tissue block?
Answer: We have performed limited testing using OCT-embedded tissue for Single Cell Gene Expression experiments. In those tests, 3-4, 100µm sections were collected from a fresh-frozen OCT-embedded mouse brain and human breast cancer tissue blocks. OCT was physically removed from the tissue using cold forceps, followed by nuclei isolation using the customer-developed Frankenstein protocol (protocol found on our webpage of Community Developed Protocols). The Frankenstein protocol was chosen because it has been optimized for isolating nuclei from frozen tissues and because it includes filtration and flow sorting steps, which are essential to clean up the nuclei suspension.
If performing both Spatial and Single Cell Gene Expression on the same fresh frozen OCT-embedded tissue block, we would recommend acquiring good sections for Visium first, before collecting sections for Single Cell Gene Expression, as tissue collection for nuclei isolation may lead to exhaustion of the tissue block for smaller samples.
Product: Visium for fresh-frozen, Single Cell Gene Expression