Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.

40Characterizing the transcriptome of individual cells is fundamental to understanding complex 41 biological systems. We describe a droplet-based system that enables 3' mRNA counting of up 56peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/065912 doi: bioRxiv preprint first posted online 84 RESULTS 86Droplet-based platform enables barcoding of tens of thousands of cells 88The scRNA-seq microfluidics platform builds on the GemCode ® technology, which has 89 been used for genome haplotyping, structural variant analysis and de novo assembly of a 90human genome [10][11][12] . The core of the technology is a Gel bead in Emulsion (GEM). GEM 91 peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/065912 doi: bioRxiv preprint first posted online 5 generation takes place in an 8-channel microfluidic chip that encapsulates single gel beads at ~80% fill rate (Fig. 1a-c). Each gel bead is functionalized with barcoded oligonucleotides that 93 consist of: i) sequencing adapters and primers, ii) a 14bp barcode drawn from ~750,000 94 designed sequences to index GEMs, iii) a 10bp randomer to index molecules (unique molecular 95 identifier, UMI), and iv) an anchored 30bp oligo-dT to prime poly-adenylated RNA transcripts 96 (Fig. 1d). Within each microfluidic channel, ~100,000 GEMs are formed per ~6-min run, 97encapsulating thousands of cells in GEMs. Cells are loaded at a limiting dilution to minimize co- 98occurrence of multiple cells in the same GEM. 100Cell lysis begins immediately after encapsulation. Gel beads automatically dissolve to 101 release their oligonucleotides for reverse transcription of poly-adenylated RNAs. Each cDNA 102 molecule contains a UMI and shared barcode per GEM, and ends with a template switching 103 oligo at the 3' end (Fig. 1e). Next, the emulsion is broken and barcoded cDNA is pooled for 104PCR amplification, using primers complementary to the switch oligos and sequencing adapters. Methods, Fig. 1f). Briefly, 98-nt of Read1s were aligned against the union of human (hg19) 123peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/065912 doi: bioRxiv preprint first posted online 6 Based on the distribution of total UMI counts for each barcode (Online Methods), we 124 estimated that 1,012 GEMs contained cells, of which 482 and 538 contained reads that mapped 125 primarily to the human and mouse transcriptome, respectively (and will be referred to as human 126 and mouse GEMs) (Fig. 2a). >83% of UMI counts were associated with cell barcodes, 127indicating low background of cell-free RNA. Eight cell-containing GEMs had a substantial 128 fraction of human and mouse UMI counts (the UMI count is >1% of each species' UMI...

SUMMARY In vitro cancer cultures, including 3-dimensional organoids, typically contain exclusively neoplastic epithelium but require artificial reconstitution to recapitulate the tumor microenvironment (TME). The co-culture of primary tumor epithelia with endogenous, syngeneic tumor-infiltrating lymphocytes (TILs) as a cohesive unit has been particularly elusive. Here, an air-liquid interface (ALI) method propagated Patient-Derived Organoids (PDOs) from >100 human biopsies or mouse tumors in syngeneic immunocompetent hosts as tumor epithelia with native embedded immune cells (T, B, NK, macrophages). Robust droplet-based, single cell simultaneous determination of gene expression and immune repertoire indicated that PDO TILs accurately preserved the original tumor T cell receptor (TCR) spectrum. Crucially, human and murine PDOs successfully modeled immune checkpoint blockade (ICB) with anti-PD-1- and/or anti-PD-L1 expanding and activating tumor antigen-specific TILs and eliciting tumor cytotoxicity. Organoid-based propagation of primary tumor epithelium en bloc with endogenous immune stroma should enable immunooncology investigations within the TME and facilitate personalized immunotherapy testing.

We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art methods. We show that SIMLR is scalable and greatly enhances clustering performance while improving the visualization and interpretability of single-cell sequencing data.

Conventional mouse and human embryonic stem cells (ESCs) can be typically derived by in vitro culture of blastocysts (Martin, 1981;Thomson et al., 1998), and induced pluripotent stem cells (iPSCs) can be generated by reprogramming somatic cells using defined genetic transduction methods (Takahashi et al., 2007;Takahashi and Yamanaka, 2006;Yu et al., 2007). In both cases, different signaling pathways appear to regulate pluripotency with different characteristics in the two species. However, while rat ESClike cells have been established based on certain traits (Demers et al., 2007;Ruhnke et al., 2003;Schulze et al., 2006;Ueda et al., 2008), to date, these lines fall short of exhibiting true pluripotency (e.g., fail to form teratoma or no/little contribution to chimerism) and thus cannot be considered authentic rat ESCs. Here, we reveal combined genetic reprogramming and chemical conditions that generate and maintain rat iPSCs (riPSCs) that can give rise to teratomas and contribute extensively to chimeric rats. The same strategy is also sufficient to generate atypical human iPSCs (hiPSCs) that exhibit similar colony morphology and self-renewal requirements/signaling responses as those of mESCs.Pluripotent stem cells have also been derived from the postimplantation egg cylinder stage epiblasts of mouse and rat (Brons et al., 2007;Tesar et al., 2007). These populations have been termed epiblast stem cells (EpiSCs). EpiSCs seem to correspond very closely to conventional hESCs with respect to colony morphology and the culture/ signaling requirements that maintain pluripotency but exhibit a range of significant phenotypic and signaling response differences from conventional mESCs. For