Detection of nuclease edited sequences in automated modules and instruments

An automated stand-alone multi-module cell editing instrument comprising:

• a housing configured to house all or some of the modules;
• a receptacle configured to receive cells;
• a receptacle configured to receive editing nucleic acids;
• a growth module for growing cells;
• a filtration module for concentrating and rendering cells electrocompetent;
• a transformation module configured to introduce the editing nucleic acids into the cells;
• a singulation and editing module configured to isolate the transformed cells and allow the editing nucleic acids to edit nucleic acids in the cells wherein the singulation and editing module comprises a device for emulsion formation, comprising:
• a microfluidic device having an emulsion formation unit including a sample well configured to receive cells in aqueous medium;
• a carrier fluid well configured to receive a fluid that is immiscible with the cells in aqueous medium;
• a collection substrate to collect aqueous droplets formed in the immiscible fluid;
• a sample channel extending from the sample well to a channel intersection;
• a carrier fluid channel extending from the carrier fluid well to the channel intersection;
• a droplet channel extending from the channel intersection to the collection substrate;
• and a pneumatic assembly having a pressure source and a pressure sensor, wherein the pneumatic assembly is configured (a) to apply pressure to the emulsion formation unit to drive generation of droplets at the channel intersection of the emulsion formation unit and collect droplets in the collection substrate, (b) to monitor the pressure with the pressure sensor, and (c) to stop application of the pressure to the emulsion formation unit when the pressure sensor detects a change in pressure indicative of air entering the sample channel from the sample well;
• a processor configured to operate the automated multi-module cell editing instrument based on user input and/or selection of a pre-programmed script;
• and
• an automated liquid handling system to move liquids from the cell receptacle to the growth module, from the growth module to the filtration module, from the filtration module to the transformation module, from the nucleic acid receptacle to the transformation module, and from the transformation module to the singulation and editing module without user intervention.