Single-cell barcoding and sequencing using droplet microfluidics

By R. Zilionis, J. Nainys, A. Veres, Virginia Savova, D. Zemmour, Allon M. Klein, L. Mazutis. Nature Protocols, 2016

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Integrating single-cell transcriptomic data across different conditions, technologies, and species (2018, neutral): “maxu, vu T X T Yv subject to u 2 ≤ 1, v 2 ≤ 1 (2)”
Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species (2019, methodology): “—scRNAseq was performed using inDrop as described previously (Zilionis et al., 2017), with modifications to DNA primers indicated in Table S6.”
zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs (2017, neutral): “Furthermore, zUMIs is exible with respect to the length and sequences of the BCs and UMIs, supporting protocols that have both sequences in one read [17, 18, 13, 15, 3, 2, 12] as well as protocols that provide UMI and BC in separate reads [19, 20, 21].”
SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data (2018, positive): “Droplet-based single-cell RNA sequencing (scRNA-seq) has enabled quantification of the transcriptomes of hundreds of thousands of cells in single experiments [1, 2].”
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation (2017, background): “Improvements in biochemistry 11, 12 and microfluidics 13, 14 continue to increase the number of cells and transcripts profiled per experiment.”