Abstract
The transcriptome and proteome encode distinct information that is important for characterizing heterogeneous biological systems. We demonstrate a method to simultaneously characterize the transcriptomes and proteomes of single cells at high throughput using aptamer probes and droplet-based single cell sequencing. With our method, we differentiate distinct cell types based on aptamer surface binding and gene expression patterns. Aptamers provide advantages over antibodies for single cell protein characterization, including rapid, in vitro, and high-purity generation via SELEX, and the ability to amplify and detect them with PCR and sequencing.
Highlights
Cellular differentiation restricts the genetic programs that cells may execute, endowing distinct functions and phenotypes[1,2]
Abseq replaces the mass tags with nucleic acid sequence tags, using droplet-based single cell sequencing for the readout[26]
Aptamers are nucleic acids that adopt a three-dimensional fold and bind to protein epitopes and small molecules[34,36]. They can be used in combination for multiplexed characterization[42], while being identified via nucleic acid sequencing
Summary
Cellular differentiation restricts the genetic programs that cells may execute, endowing distinct functions and phenotypes[1,2]. High throughput single cell transcriptome sequencing[12,13,14] is an effective tool for deconvoluting heterogeneity because it provides ample information to identify cell type[15] and infer cell state and function[16]. The microfluidic approaches used to sequence single cell mRNA can be applied to the tags, allowing simultaneous surface and transcriptome profiling of single cells at high throughput[27,28] While this provides exciting opportunities for characterizing cells with paired gene expression and protein data, it requires access to high-affinity antibodies. SELEX can be applied directly to living cells, avoiding antigen purification, and shortening the process from months to weeks[38,39,40] This simplifies affinity reagent generation and enables new surface characterization only accessible to aptamers[41]. We demonstrate Apt-seq by using it to discriminate between cells based on aptamer binding and differences in gene expression
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