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Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;MIT, Dept Chem, Cambridge, MA 02139 USA.;Broad Inst MIT & Harvard, Cambridge, MA USA.;MIT, Ragon Inst Massachusetts Gen Hosp, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard Univ, Cambridge, MA 02138 USA..
Broad Inst MIT & Harvard, Cambridge, MA USA..
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala Univ, Sci Life Lab, Uppsala, Sweden.;Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA.;Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA.;Howard Hughes Med Inst, Stanford, CA USA..
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2016 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 17, 188Article in journal (Refereed) Published
Abstract [en]

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 (TM) 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.

Place, publisher, year, edition, pages
2016. Vol. 17, 188
Keyword [en]
Single-cell transcriptomics, Single-cell proteomics, Single-cell multi-omics, Proximity extension assay, Metadata
National Category
Medical Genetics Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
URN: urn:nbn:se:uu:diva-305451DOI: 10.1186/s13059-016-1045-6ISI: 000383428600001PubMedID: 27640647OAI: oai:DiVA.org:uu-305451DiVA: diva2:1038668
Funder
NIH (National Institute of Health), P50HG006193; U24AI11862-01; DP2OD020839EU, FP7, Seventh Framework Programme, 259796; 294409Swedish Research CouncilSwedish Society for Medical Research (SSMF)
Available from: 2016-10-19 Created: 2016-10-18 Last updated: 2016-10-19Bibliographically approved

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Gallant, Caroline J.Landegren, Ulf
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Department of Immunology, Genetics and PathologyScience for Life Laboratory, SciLifeLab
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