Input nuclei suspension should contain >90% dead cells with intact nuclei. The presence of a high fraction of dying cells with damaged nuclei per ambient RNA and cellular debris may influence sequencing performance
There are various types of lysis buffer that can be used to lyse the cells and release the nuclei. This very much depends on the tissue type. The basic buffer can either be hypotonic (which might help lyse the cells and release the nuclei) or isotonic (which may be more intrinsically gentle for the preparation). The detergent that is used to lyse the cells can be varied (as well as the concentration). Commonly used buffers alternative to the one we used are:
Lysis buffer NST (isotonic+NP40)
Lysis buffer IST (hypotonic + NP40)
For every type of tissue, the number of strokes with the dounce homogenizer needs to be calibrated. The incubation time after the dounce homogenization can also be varied. For each tissue an optimization needs to be performed.
Nuclei as opposed to cells are problematic since they are smaller and they are more sticky because of DNA leakage and other factors. This means that there is much more significant loss after each centrifugation step. To try to minimize the loss, we have tried various methods to prevent the nuclei sticking to the sides of the tubes. One that work and we recommend is the coating of the tubes for about one hour before use with PBS+1%BSA. Recently, we have tried using polystyrene 5ml FACS tubes but we cannot comment if they are any better at reducing loss.