The number of nuclei obtained per scroll can vary by block and depends on the scroll thickness. We provide the table below as a starting point for customers in the EvercodeTM FFPE Nuclei Preparation User Guide. The values shown in the table are based on historical experimental data generated using FFPE tissue samples with approximate dimensions of ~10 mm × 5 mm. In these experiments, our team observed average yields of ~300,000 nuclei from 25 µm scrolls and ~600,000-900,000 nuclei from 50 µm scrolls.
While there is no defined minimum number of nuclei required for the Evercode FFPE Nuclei Preparation Kit, we recommend starting with a 25 µm tissue scroll. Based on our internal experience, this input thickness typically produces around ~300,000 nuclei for samples of the dimensions described above and provides a good starting point for most workflows. Factors such as necrosis, inflammation, and tissue type can impact yield. For optimal results, it is ideal to begin pre-barcoding FFPE sample preparation with at least ~50,000 high-quality dissociated nuclei per sample. The number of nuclei required for input into the Evercode FFPE WT kit depends on the kit size. Please see Evercode WT FFPE Sample Loading Tables for more information.