PT  - JOURNAL ARTICLE
AU  - Jamie L. Marshall
AU  - Benjamin R. Doughty
AU  - Vidya Subramanian
AU  - Qingbo Wang
AU  - Linlin M. Chen
AU  - Samuel G. Rodriques
AU  - Kaite Zhang
AU  - Philine Guckelberger
AU  - Charles P. Fulco
AU  - Joseph Nasser
AU  - Elizabeth J. Grinkevich
AU  - Teia Noel
AU  - Sarah Mangiameli
AU  - Anna Greka
AU  - Eric S. Lander
AU  - Fei Chen
AU  - Jesse M. Engreitz
TI  - HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes
AID  - 10.1101/2020.06.01.128314
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.01.128314
4099  - http://biorxiv.org/content/early/2020/06/02/2020.06.01.128314.short
4100  - http://biorxiv.org/content/early/2020/06/02/2020.06.01.128314.full
AB  - Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of up to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq, making HyPR-seq a powerful method for targeted RNA profiling in single cells.Competing Interest StatementF.C., J.M.E., J.L.M., V.S., and S.R. are inventors on patent applications filed by the Broad Institute related to this work (62/676,069 and 62/780,889). E.S.L. serves on the Board of Directors for Codiak BioSciences and Neon Therapeutics, and serves on the Scientific Advisory Board of F-Prime Capital Partners and Third Rock Ventures; he is also affiliated with several non-profit organizations including serving on the Board of Directors of the Innocence Project, Count Me In, and Biden Cancer Initiative, and the Board of Trustees for the Parker Institute for Cancer Immunotherapy. He has served and continues to serve on various federal advisory committees.