Abstract
Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput methods are needed for capturing the unbiased diversity of cells. Droplet microfluidics is among the most promising candidates for capturing and processing thousands of individual cells for whole-transcriptome or genomic analysis in a massively parallel manner with minimal reagent use. We recently established a method called inDrops, which has the capability to index >15,000 cells in an hour. A suspension of cells is first encapsulated into nanoliter droplets with hydrogel beads (HBs) bearing barcoding DNA primers. Cells are then lysed and mRNA is barcoded (indexed) by a reverse transcription (RT) reaction. Here we provide details for (i) establishing an inDrops platform (1 d); (ii) performing hydrogel bead synthesis (4 d); (iii) encapsulating and barcoding cells (1 d); and (iv) RNA-seq library preparation (2 d). inDrops is a robust and scalable platform, and it is unique in its ability to capture and profile >75% of cells in even very small samples, on a scale of thousands or tens of thousands of cells.
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Acknowledgements
This work was supported by the Lithuanian-Swiss Research and Development Program (grant no. CH-3-SMM-01/03) and an Edward J Mallinckrodt Foundation Grant (to A.M.K.). L.M. holds a Marie Curie Individual Fellowship (705791). A.M.K. holds a Burroughs Wellcome Fund CASI Award. A.V. is supported by the HSCI Medical Scientist Training Fellowship and the Harvard Presidential Scholars Fund. Liquid-handling robotics was carried out at the ICCB-Longwood Screening Facility at Harvard Medical School (HMS); microfabrication was carried out at the HMS Microfabrication/Microfluidics core facility.
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Contributions
A.M.K. and L.M. developed the original inDrops method. A.M.K., A.V., and V.S. developed the bioinformatic pipeline for raw sequencing data analysis. R.Z., A.M.K., and L.M. analyzed data provided in the Anticipated Results. D.Z. designed library PCR primers and custom sequencing primers. R.Z., J.N., A.M.K., and L.M. wrote the manuscript.
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L.M. and A.M.K. are inventors on a patent application (PCT/US2015/026443) that includes some of the ideas described in this article. A.M.K. is a cofounder and science advisory board member of 1CellBio. L.M. is affiliated with Droplet Genomics. The rest of the authors declare no competing financial interests.
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Supplementary Methods 1 and 2, Supplementary Table 1, and Supplementary Figure 1 (PDF 280 kb)
Supplementary Table 2
Supplementary Tables 2 (XLSX 41 kb)
Supplementary Table 3
Supplementary Tables 3 (XLSX 45 kb)
Supplementary Table 4
Supplementary Tables 4 (XLSX 44 kb)
Supplementary Data 1
Designs for microfluidic chips. (ZIP 442 kb)
Supplementary Data 2
Hamilton Microlab STAR-let liquid handler method files. (ZIP 38 kb)
Supplementary Software
Python script for sequencing data processing. (ZIP 27 kb)
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Zilionis, R., Nainys, J., Veres, A. et al. Single-cell barcoding and sequencing using droplet microfluidics. Nat Protoc 12, 44–73 (2017). https://doi.org/10.1038/nprot.2016.154
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DOI: https://doi.org/10.1038/nprot.2016.154
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