Literature DB >> 28854175

Multiplexed quantification of proteins and transcripts in single cells.

Vanessa M Peterson1, Kelvin Xi Zhang2, Namit Kumar1, Jerelyn Wong3, Lixia Li1, Douglas C Wilson3, Renee Moore4, Terrill K McClanahan3, Svetlana Sadekova3, Joel A Klappenbach1.   

Abstract

We present a tool to measure gene and protein expression levels in single cells with DNA-labeled antibodies and droplet microfluidics. Using the RNA expression and protein sequencing assay (REAP-seq), we quantified proteins with 82 barcoded antibodies and >20,000 genes in a single workflow. We used REAP-seq to assess the costimulatory effects of a CD27 agonist on human CD8+ lymphocytes and to identify and characterize an unknown cell type.

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Year:  2017        PMID： 28854175     DOI： 10.1038/nbt.3973

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  30 in total

1.  Purification of hematopoietic stem cells for further biological study.

Authors:  T E Thomas; C L Miller; C J Eaves
Journal:  Methods       Date:  1999-03       Impact factor: 3.608

2.  OSA: a fast and accurate alignment tool for RNA-Seq.

Authors:  Jun Hu; Huanying Ge; Matt Newman; Kejun Liu
Journal:  Bioinformatics       Date:  2012-05-15       Impact factor: 6.937

3.  STAR: ultrafast universal RNA-seq aligner.

Authors:  Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras
Journal:  Bioinformatics       Date:  2012-10-25       Impact factor: 6.937

4.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

5.  Prospective isolation of human clonogenic common myeloid progenitors.

Authors:  Markus G Manz; Toshihiro Miyamoto; Koichi Akashi; Irving L Weissman
Journal:  Proc Natl Acad Sci U S A       Date:  2002-08-22       Impact factor: 11.205

6.  Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.

Authors:  Alexandra-Chloé Villani; Rahul Satija; Gary Reynolds; Siranush Sarkizova; Karthik Shekhar; James Fletcher; Morgane Griesbeck; Andrew Butler; Shiwei Zheng; Suzan Lazo; Laura Jardine; David Dixon; Emily Stephenson; Emil Nilsson; Ida Grundberg; David McDonald; Andrew Filby; Weibo Li; Philip L De Jager; Orit Rozenblatt-Rosen; Andrew A Lane; Muzlifah Haniffa; Aviv Regev; Nir Hacohen
Journal:  Science       Date:  2017-04-21       Impact factor: 47.728

7.  Genomic variation. Impact of regulatory variation from RNA to protein.

Authors:  Alexis Battle; Zia Khan; Sidney H Wang; Amy Mitrano; Michael J Ford; Jonathan K Pritchard; Yoav Gilad
Journal:  Science       Date:  2014-12-18       Impact factor: 47.728

8.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Authors:  Bo Li; Colin N Dewey
Journal:  BMC Bioinformatics       Date:  2011-08-04       Impact factor: 3.307

9.  Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells.

Authors:  Spyros Darmanis; Caroline Julie Gallant; Voichita Dana Marinescu; Mia Niklasson; Anna Segerman; Georgios Flamourakis; Simon Fredriksson; Erika Assarsson; Martin Lundberg; Sven Nelander; Bengt Westermark; Ulf Landegren
Journal:  Cell Rep       Date:  2015-12-31       Impact factor: 9.423

10.  Characterization of the human T cell response to in vitro CD27 costimulation with varlilumab.

Authors:  Venky Ramakrishna; Karuna Sundarapandiyan; Biwei Zhao; Max Bylesjo; Henry C Marsh; Tibor Keler
Journal:  J Immunother Cancer       Date:  2015-08-18       Impact factor: 13.751
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  247 in total

1.  Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry.

Authors:  Karolyn A Oetjen; Katherine E Lindblad; Meghali Goswami; Gege Gui; Pradeep K Dagur; Catherine Lai; Laura W Dillon; J Philip McCoy; Christopher S Hourigan
Journal:  JCI Insight       Date:  2018-12-06

2.  SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.

Authors:  Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker
Journal:  J Immunother Cancer       Date:  2020-12       Impact factor: 13.751

3.  Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells.

Authors:  Arnav Moudgil; Michael N Wilkinson; Xuhua Chen; June He; Alexander J Cammack; Michael J Vasek; Tomás Lagunas; Zongtai Qi; Matthew A Lalli; Chuner Guo; Samantha A Morris; Joseph D Dougherty; Robi D Mitra
Journal:  Cell       Date:  2020-07-24       Impact factor: 41.582

Review 4.  Single Cell RNA Sequencing in Atherosclerosis Research.

Authors:  Jesse W Williams; Holger Winkels; Christopher P Durant; Konstantin Zaitsev; Yanal Ghosheh; Klaus Ley
Journal:  Circ Res       Date:  2020-04-23       Impact factor: 17.367

5.  Single Cell Genomics for Tumor Heterogeneity.

Authors:  Hae-Ock Lee; Woong-Yang Park
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

Review 6.  Single cell protein analysis for systems biology.

Authors:  Ezra Levy; Nikolai Slavov
Journal:  Essays Biochem       Date:  2018-10-26       Impact factor: 8.000

Review 7.  Tumour heterogeneity and metastasis at single-cell resolution.

Authors:  Devon A Lawson; Kai Kessenbrock; Ryan T Davis; Nicholas Pervolarakis; Zena Werb
Journal:  Nat Cell Biol       Date:  2018-11-26       Impact factor: 28.824

Review 8.  The role of systems biology approaches in determining molecular signatures for the development of more effective vaccines.

Authors:  Abdulmohammad Pezeshki; Inna G Ovsyannikova; Brett A McKinney; Gregory A Poland; Richard B Kennedy
Journal:  Expert Rev Vaccines       Date:  2019-02-11       Impact factor: 5.217

Review 9.  Revolutionizing Cancer Immunology: The Power of Next-Generation Sequencing Technologies.

Authors:  Meromit Singer; Ana C Anderson
Journal:  Cancer Immunol Res       Date:  2019-02       Impact factor: 11.151

Review 10.  Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?

Authors:  Megan Crow; Jesse Gillis
Journal:  Trends Genet       Date:  2018-08-23       Impact factor: 11.639
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