Hypr-Seq: Single-Cell Quantification of Chosen Rnas Via Hybridization and Sequencing of DNA Probes
HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes Jamie L. Marshalla,1, Benjamin R. Doughtya,1, Vidya Subramaniana, Philine Guckelbergera,b, Qingbo Wanga,c,d, Linlin M. Chena, Samuel G. Rodriquesa,e,f,2, Kaite Zhanga, Charles P. Fulcoa,3, Joseph Nassera, Elizabeth J. Grinkevicha, Teia Noela, Sarah Mangiamelia, Drew T. Bergmana, Anna Grekaa,g, Eric S. Landera,h,i,4,5, Fei Chena,4,5, and Jesse M. Engreitza,j,k,4,5 aBroad Institute of MIT and Harvard, Cambridge, MA 02142; bDepartment of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; cAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114; dProgram in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115; eDepartment of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139; fMIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139; gDepartment of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115; hDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115; iDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; jDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305; and kBasic Science and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford University School of Medicine, Stanford, CA 94305 Contributed by Eric S. Lander, November 9, 2020 (sent for review May 29, 2020; reviewed by Alexander Meissner, Kathrin Plath, and Chun J. Ye) Single-cell quantification of RNAs is important for understanding and quantify specific transcripts in single cells, for example using cellular heterogeneity and gene regulation, yet current approaches target-specific reverse transcription of RNA during library prep- suffer from low sensitivity for individual transcripts, limiting their aration (13–15) or hybrid selection, PCR, or linear amplification utility for many applications.
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