Multiplex identification of proteins using a neural network–based spectral analysis.

Abstract

(A) Experimental design of a co-seeding assay including 11 different cell types, labeled with specific nanobarcodes (see Methods section for details). (B) Example of an Nrxn-2ß (SS#4(+))/Nlgn-1 (SS#AB) and an Nrxn-2ß (SS#4(−))/Nlgn-2 (−) pair (red boxes depict typical cell contacts). (C) Overlay of cells containing nanobarcode proteins and Nrxn- or Nlgn-positive cells. Nanobarcode proteins are shown in green (anti-ALFA-Atto488). Nrxn or Nlgn isoforms are shown in magenta (anti-HA and anti-goat-Cy3). See S21 Fig for example images of all proteins. Scale bars: 20 μm. (D) Interaction preferences of Nrxn/Nlgn isoforms. A total of 4,569 cell contacts, 147 images, 4 independent co-seeding experiments. The Nrxn/Nlgn codes, such as SS#4(+) refer to the respective splicing sites of the proteins, according to the literature (e.g., [24]). The data underlying this Figure can be found in the S1 Data file, Sheet “Fig 4D”, available from http://dx.doi.org/10.17169/refubium-40101.</p