Abstract
Drop-Seq is a low-cost, high-throughput platform to profile thousands of cells by encapsualting them into individual droplets. Uniquely barcoded mRNA capture microparticles and cells are coconfined through a microfluidic device within the droplets where they undergo cell lysis and RNA hybridiztion. After breaking the droplets and pooling the hybridized particles, reverse transcription, PCR, and sequencing in single reactions allow to generate data from thousands of single-cell transcriptomes while maintaining information on the cellular origin of each transcript.
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References
Kolodziejczyk AA, Kim JK, Svensson V et al (2015) The technology and biology of single-cell RNA sequencing. Mol Cell 58:610–620
Kolodziejczyk AA, Lönnberg T (2018) Global and targeted approaches to single-cell transcriptome characterization. Brief Funct Genomics 17:209–219
Svensson V, Vento-Tormo R, Teichmann SA (2018) Exponential scaling of single-cell RNA-seq in the past decade. Nat Protoc 13:599–604
Ziegenhain C, Vieth B, Parekh S et al (2017) Comparative analysis of single-cell RNA sequencing methods. Mol Cell 65:631–643.e4
Tang F, Barbacioru C, Wang Y et al (2009) mRNA-seq whole-transcriptome analysis of a single cell. Nat Methods 6:377–382
Macaulay IC, Svensson V, Labalette C et al (2016) Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells. Cell Rep 14:966–977
Shalek AK, Satija R, Adiconis X et al (2013) Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498:236–240
Zheng GXY, Terry JM, Belgrader P et al (2017) Massively parallel digital transcriptional profiling of single cells. Nat Commun 8:14049
Macosko EZ, Basu A, Satija R et al (2015) Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161:1202–1214
Klein AM, Mazutis L, Akartuna I et al (2015) Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161:1187–1201
Habib N, Avraham-Davidi I, Basu A et al (2017) Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods 14:955–958
Stoeckius M, Hafemeister C, Stephenson W et al (2017) Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 14:865–868
Lo YMD, Chan KCA (2006) Setting up a polymerase chain reaction laboratory. In: Lo YMD, Chiu RWK, Chan KCA (eds) Clinical applications of PCR. Humana, Totowa, NJ, pp 11–18
McCarroll S (2018) Drop-seq-protocol-v3.1-Dec-2015. McCarroll Lab, Boston, MA. http://mccarrolllab.com/dropseq/
Acknowledgments
J.B. was supported by a research stipend from the Fritz Thyssen Foundation. G.R. was supported by the Intramural Research Program of the Division of Intramural Research Z01AI000947, NIAID, NIH; the UCLA-Caltech MSTP, and the NIGMS T32 GM008042.
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Bageritz, J., Raddi, G. (2019). Single-Cell RNA Sequencing with Drop-Seq. In: Proserpio, V. (eds) Single Cell Methods. Methods in Molecular Biology, vol 1979. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9240-9_6
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DOI: https://doi.org/10.1007/978-1-4939-9240-9_6
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