Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
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 Fluidig...
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| Format: | Article |
| Language: | English |
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BioMed Central
2016
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| Online Access: | http://hdl.handle.net/1721.1/105800 https://orcid.org/0000-0003-3079-5134 https://orcid.org/0000-0002-5621-8768 https://orcid.org/0000-0002-8279-7150 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1826215398992773120 |
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| author | Li, Shuqiang Darmanis, Spyros Lundberg, Martin Fredriksson, Simon Landegren, Ulf Gallant, Caroline J. Livak, Kenneth J. Genshaft, Alex S. Prakadan, Sanjay Ziegler, Carly Hong, Joyce Regev, Aviv Shalek, Alexander K |
| author2 | Massachusetts Institute of Technology. Institute for Medical Engineering & Science |
| author_facet | Massachusetts Institute of Technology. Institute for Medical Engineering & Science Li, Shuqiang Darmanis, Spyros Lundberg, Martin Fredriksson, Simon Landegren, Ulf Gallant, Caroline J. Livak, Kenneth J. Genshaft, Alex S. Prakadan, Sanjay Ziegler, Carly Hong, Joyce Regev, Aviv Shalek, Alexander K |
| author_sort | Li, Shuqiang |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T16:27:17Z |
| format | Article |
| id | mit-1721.1/105800 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T16:27:17Z |
| publishDate | 2016 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | mit-1721.1/1058002022-09-29T19:54:03Z Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction Li, Shuqiang Darmanis, Spyros Lundberg, Martin Fredriksson, Simon Landegren, Ulf Gallant, Caroline J. Livak, Kenneth J. Genshaft, Alex S. Prakadan, Sanjay Ziegler, Carly Hong, Joyce Regev, Aviv Shalek, Alexander K Massachusetts Institute of Technology. Institute for Medical Engineering & Science Harvard University--MIT Division of Health Sciences and Technology Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Chemistry Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Ragon Institute of MGH, MIT and Harvard Koch Institute for Integrative Cancer Research at MIT Genshaft, Alex S. Prakadan, Sanjay Ziegler, Carly Hong, Joyce Regev, Aviv Shalek, Alexander K 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. Searle Scholars Program Arnold and Mabel Beckman Foundation. Beckman Young Investigator National Institutes of Health (U.S.) (Center for Excellence in Genomic Sciences. Grant P50HG006193) Klarman Cell Observatory National Institutes of Health (U.S.) (Grant U24AI11862-01) Howard Hughes Medical Institute National Institute of General Medical Sciences (U.S.) (Award T32GM007753) National Institutes of Health (U.S.) (New Innovator Award DP2OD020839) 2016-12-12T21:14:31Z 2016-12-12T21:14:31Z 2016-09 2016-07 2016-09-20T03:37:14Z Article http://purl.org/eprint/type/JournalArticle 1474-760X http://hdl.handle.net/1721.1/105800 Genshaft, Alex S et al. “Multiplexed, Targeted Profiling of Single-Cell Proteomes and Transcriptomes in a Single Reaction.” Genome Biology 17.1 (2016): n. pag. https://orcid.org/0000-0003-3079-5134 https://orcid.org/0000-0002-5621-8768 https://orcid.org/0000-0002-8279-7150 https://orcid.org/0000-0001-8567-2049 en http://dx.doi.org/10.1186/s13059-016-1045-6 Genome Biology Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ The Author(s). application/pdf BioMed Central BioMed Central |
| spellingShingle | Li, Shuqiang Darmanis, Spyros Lundberg, Martin Fredriksson, Simon Landegren, Ulf Gallant, Caroline J. Livak, Kenneth J. Genshaft, Alex S. Prakadan, Sanjay Ziegler, Carly Hong, Joyce Regev, Aviv Shalek, Alexander K Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction |
| title | Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction |
| title_full | Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction |
| title_fullStr | Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction |
| title_full_unstemmed | Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction |
| title_short | Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction |
| title_sort | multiplexed targeted profiling of single cell proteomes and transcriptomes in a single reaction |
| url | http://hdl.handle.net/1721.1/105800 https://orcid.org/0000-0003-3079-5134 https://orcid.org/0000-0002-5621-8768 https://orcid.org/0000-0002-8279-7150 https://orcid.org/0000-0001-8567-2049 |
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