Extended Data Fig. 1: The CARMEN workflow at the molecular and macroscopic scale.

a, Detailed molecular schematic of nucleic acid detection in CARMEN–Cas13. After amplification (with optional reverse transcription), detection is performed with Cas13, using in vitro transcription to convert amplified DNA into RNA. The resulting RNA is detected with exquisite sequence specificity by Cas13–crRNA complexes, and collateral cleavage activity of Cas13 produces a signal using a cleavage reporter RNA. b, Overview of the CARMEN workflow. Amplified samples and detection mixes are colour coded, emulsified and pooled into one tube. In a single pipetting step, the pool of droplets is loaded onto a chip, where the droplets self-organize into pairs. Fluorescence microscopy is used to read the colour code of each droplet, mapping the position of each sample and detection mix in the chip and droplets in each well are merged, initiating all reactions across the chip nearly instantaneously. After incubation, the reaction result for each well is read using fluorescence microscopy and mapped back to the colour codes of the sample and/or detection mix in each well. c, Microwell design optimized for droplets made from PCR products or detection mixes. d, Dimensions and layout of a standard chip. The area covered by the microwell array is shown in light blue. e, Photograph of a standard chip. f, Photograph of a standard chip sealed inside an acrylic loader, ready for imaging.