Detection of nuclease edited sequences in automated modules and instruments

A method for isolating and editing cells in an automated stand-alone multi-module cell editing instrument, comprising the steps of:

• providing live cells in a receptacle configured to receive the live cells;
• providing editing nucleic acids the receptacle configured to receive editing nucleic acids;
• growing the live cells in a growth module to a desired optical density to produce grown cells;
• transforming the grown cells in a transformation module configured to introduce editing nucleic acids into the grown cells to produce transformed cells;
• providing the transformed cells to an editing module at a dilution resulting in substantially isolated transformed cells in an appropriate liquid growth medium comprising 0.25%-6% alginate, wherein the substantially isolated transformed cells comprise nucleic acid-guided nuclease editing components;
• solidifying the alginate-containing medium with a divalent cation;
• providing conditions to allow editing to take place in the substantially isolated transformed cells to produce edited cells allowing the edited cells to grow for 2 to 50 doublings to establish cell colonies;
• allowing the cell colonies to grow to become normalized;
• liquefying the alginate-containing medium with a divalent cation chelating agent;
• and
• using an automated liquid handling system to 1) transfer the editing nucleic acids from receptacle configured to receive nucleic acids to the transformation module, 2) transfer the live cells from the receptacle configured to receive the live cells to the growth module, 3) transfer the grown cells from the growth module to the transformation module;
• and 4) transfer the transformed cells from the transformation module to the editing module, without user intervention.