A 
system, methods, and apparatus are described to collect and prepare single cells, nuclei, subcellular components, and biomolecules from specimens including tissues. The 
system can perform enzymatic and / or physical disruption of the tissue to dissociate it into single-cells or nuclei in suspension or subcellular components including nucleic acids. In some embodiments, the 
titer of dissociated cells is monitored at intervals and the viability determined. In some embodiments, the 
processing is adjusted according to the measurements of the 
titer and viability. In some embodiments, the single-cells or nuclei in suspension are washed and resuspended in the buffer or media of choice. In some embodiments, the conditions are chosen to produce nuclei. In other embodiments, the single-cells or nuclei are purified by affinity paramagnetic bead 
processing. In some embodiments, matched bulk 
nucleic acid to the single-cells is produced. In other embodiments, single-
cell libraries, or nuclei libraries, or matched bulk libraries, or bulk libraries are produced. The single cells or nuclei can then be further processed by FACS, 
DNA sequencing, 
mass spectrometry, 
fluorescence, or other methods. In other embodiments, the 
tissue processing is integrated with an analytical 
system to produce a sample-to-answer system such as a tissue-to-
genomics system.