Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction.

Genome Biol
Authors
Abstract

We present a scalable, integrated strategy for coupled protein and RNA detection from single cells. Our approach leverages the DNA polymerase activity of reverse transcriptase to simultaneously perform proximity extension assays and complementary DNA synthesis in the same reaction. Using the Fluidigm C1™ system, we profile the transcriptomic and proteomic response of a human breast adenocarcinoma cell line to a chemical perturbation, benchmarking against in situ hybridizations and immunofluorescence staining, as well as recombinant proteins, ERCC Spike-Ins, and population lysate dilutions. Through supervised and unsupervised analyses, we demonstrate synergies enabled by simultaneous measurement of single-cell protein and RNA abundances. Collectively, our generalizable approach highlights the potential for molecular metadata to inform highly-multiplexed single-cell analyses.

Year of Publication
2016
Journal
Genome Biol
Volume
17
Issue
1
Pages
188
Date Published
2016 Sep 19
ISSN
1474-760X
DOI
10.1186/s13059-016-1045-6
PubMed ID
27640647
PubMed Central ID
PMC5027636
Links
Grant list
P50 HG006193 / HG / NHGRI NIH HHS / United States
T32 GM007753 / GM / NIGMS NIH HHS / United States