Nucleic acid-guided editing of exogenous polynucleotides in heterologous cells

A method of nucleic acid-guided nuclease editing of five hundred or more exogenous target polynucleotides from source cells within heterologous editing cells in a single multiplexed automated operation, comprising:

• inserting five hundred or more exogenous target polynucleotides from the source cells into shuttle vector backbones to form a library of shuttle vectors;
• transforming heterologous editing cells with the library of shuttle vectors to produce first transformed heterologous editing cells;
• transferring the first transformed heterologous editing cells into a growth module;
• growing the first transformed heterologous editing cells in a growth module;
• transferring the first transformed heterologous editing cells from the growth module to a transformation module;
• providing one or more editing vectors in a first receptacle wherein the editing vectors comprise a coding sequence for a nuclease, a guide nucleic acid and a DNA donor sequence, and wherein the one or more editing vectors target one or more of the exogenous target polynucleotides;
• transferring the one or more editing vectors from the first receptacle to the transformation module;
• introducing the one or more editing vectors into the first transformed heterologous editing cells in the transformation module to produce second transformed heterologous editing cells;
• transferring the second transformed heterologous editing cells from the transformation module to an editing module;
• allowing editing to take place in the editing module under conditions that allow the editing vectors to edit the exogenous target polynucleotides in the second transformed heterologous editing cells thereby forming edited cells;
• isolating the edited cells;
• and
• isolating the edited shuttle vectors;
• wherein the first receptacle, growth module, transformation module and editing module are all part of a stand-alone automated multi-module cell processing instrument, and wherein a liquid handling system moves the editing vectors from the first receptacle to the transformation module, and moves the first transformed heterologous editing cells from the growth module to the transformation module and from the transformation module to the editing module all without human intervention.