The subject invention provides simple and consistent methods to break suspension cell aggregates to single cells with intact primary cell walls. The subject invention relates in part to cell separation of suspension cell aggregates cultured in medium containing pectin-degrading enzymes or tubulin de-polymerizing compounds including colchicine. The subject invention also relates to novel uses of compounds for such purposes. Another aspect of the subject invention relates to transformation of the subject, isolated cells. Such processes simplify and integrate single-cell-based transformation and selection processes into transgenic and transplastomic event-generation work processes. The subject invention also removes technical constraints and produces marker-free and uniformly expressing transgenic lines in a high throughput fashion to support various needs of animal health, biopharma, and trait and crop protection platforms.