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. Author manuscript; available in PMC: 2023 Aug 1.
Published in final edited form as: Nat Genet. 2023 Jan 12;55(2):346–354. doi: 10.1038/s41588-022-01278-7

Fig. 4. scMPRA design and workflow in mouse retina.

Fig. 4.

(a) Schematic of Gnb3 promoter library constructs. In addition to the cBC and rBC barcodes, the Gnb3 promoter library contains an additional cassette in which the constitutive U6 promoter expresses a second copy of the cBC with a capture sequence for isolating these transcripts on gel beads. (b) Two different types of transcripts produced from the Gnb3 promoter library to measure promoter expression and detect unexpressed promoters respectively. The two types of transcripts originating from the same cell share the same 10x cell barcodes (c) Experimental workflow for scMPRA in ex vivo mouse retinas. (d) UMAP of all cells (n = 22161) measured in scMPRA with four major cell types identified. (e) For each Gnb3 variant in the library, we determined the proportion of cells that contain barcoded poly(A) transcripts out of all the cells that contained the variant. (f) Reproducibility of promoter activities between biological replicates in each of the four major cell types (all 115 promoters were detected in every cell type).