References

Alon, S., D. R. Goodwin, A. Sinha, A. T. Wassie, F. Chen, E. R. Daugharthy, Y. Bando, et al. 2021. “Expansion Sequencing: Spatially Precise in Situ Transcriptomics in Intact Biological Systems.” Journal Article. Science 371 (6528). https://doi.org/10.1126/science.aax2656.

Bakken, T. E., R. D. Hodge, J. A. Miller, Z. Yao, T. N. Nguyen, B. Aevermann, E. Barkan, et al. 2018. “Single-Nucleus and Single-Cell Transcriptomes Compared in Matched Cortical Cell Types.” Journal Article. PLoS One 13 (12): e0209648. https://doi.org/10.1371/journal.pone.0209648.

Becht, E., L. McInnes, J. Healy, C. A. Dutertre, I. W. H. Kwok, L. G. Ng, F. Ginhoux, and E. W. Newell. 2018. “Dimensionality Reduction for Visualizing Single-Cell Data Using UMAP.” Journal Article. Nat Biotechnol. https://doi.org/10.1038/nbt.4314.

Birnbaum, K. D. 2018. “Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues.” Journal Article. Annu Rev Genet 52: 203–21. https://doi.org/10.1146/annurev-genet-120417-031247.

Brüning, Ralf Schulze, Lukas Tombor, Marcel H. Schulz, Stefanie Dimmeler, and David John. 2021. “Comparative Analysis of Common Alignment Tools for Single Cell RNA Sequencing.” Journal Article. bioRxiv, 2021.02.15.430948. https://doi.org/10.1101/2021.02.15.430948.

Butler, A., P. Hoffman, P. Smibert, E. Papalexi, and R. Satija. 2018. “Integrating Single-Cell Transcriptomic Data Across Different Conditions, Technologies, and Species.” Journal Article. Nat Biotechnol 36 (5): 411–20. https://doi.org/10.1038/nbt.4096.

Campbell, K. R., and C. Yau. 2018. “Uncovering Pseudotemporal Trajectories with Covariates from Single Cell and Bulk Expression Data.” Journal Article. Nat Commun 9 (1): 2442. https://doi.org/10.1038/s41467-018-04696-6.

Cao, J., D. R. O’Day, H. A. Pliner, P. D. Kingsley, M. Deng, R. M. Daza, M. A. Zager, et al. 2020. “A Human Cell Atlas of Fetal Gene Expression.” Journal Article. Science 370 (6518). https://doi.org/10.1126/science.aba7721.

Cao, J., J. S. Packer, V. Ramani, D. A. Cusanovich, C. Huynh, R. Daza, X. Qiu, et al. 2017. “Comprehensive Single-Cell Transcriptional Profiling of a Multicellular Organism.” Journal Article. Science 357 (6352): 661–67. https://doi.org/10.1126/science.aam8940.

Davie, K., J. Janssens, D. Koldere, M. De Waegeneer, U. Pech, L. Kreft, S. Aibar, et al. 2018. “A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain.” Journal Article. Cell 174 (4): 982–998 e20. https://doi.org/10.1016/j.cell.2018.05.057.

Ding, J., X. Adiconis, S. K. Simmons, M. S. Kowalczyk, C. C. Hession, N. D. Marjanovic, T. K. Hughes, et al. 2020. “Systematic Comparison of Single-Cell and Single-Nucleus RNA-Sequencing Methods.” Journal Article. Nat Biotechnol 38 (6): 737–46. https://doi.org/10.1038/s41587-020-0465-8.

Du, Y., Q. Huang, C. Arisdakessian, and L. X. Garmire. 2020. “Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment.” Journal Article. G3 (Bethesda) 10 (5): 1775–83. https://doi.org/10.1534/g3.120.401160.

Gierahn, T. M., 2nd Wadsworth M. H., T. K. Hughes, B. D. Bryson, A. Butler, R. Satija, S. Fortune, J. C. Love, and A. K. Shalek. 2017. “Seq-Well: Portable, Low-Cost RNA Sequencing of Single Cells at High Throughput.” Journal Article. Nat Methods 14 (4): 395–98. https://doi.org/10.1038/nmeth.4179.

Habib, N., I. Avraham-Davidi, A. Basu, T. Burks, K. Shekhar, M. Hofree, S. R. Choudhury, et al. 2017. “Massively Parallel Single-Nucleus RNA-Seq with DroNc-Seq.” Journal Article. Nat Methods 14 (10): 955–58. https://doi.org/10.1038/nmeth.4407.

Habib, N., Y. Li, M. Heidenreich, L. Swiech, I. Avraham-Davidi, J. J. Trombetta, C. Hession, F. Zhang, and A. Regev. 2016. “Div-Seq: Single-Nucleus RNA-Seq Reveals Dynamics of Rare Adult Newborn Neurons.” Journal Article. Science 353 (6302): 925–28. https://doi.org/10.1126/science.aad7038.

Hafemeister, C., and R. Satija. 2019. “Normalization and Variance Stabilization of Single-Cell RNA-Seq Data Using Regularized Negative Binomial Regression.” Journal Article. Genome Biol 20 (1): 296. https://doi.org/10.1186/s13059-019-1874-1.

Ji, Q., Y. Zheng, G. Zhang, Y. Hu, X. Fan, Y. Hou, L. Wen, et al. 2019. “Single-Cell RNA-Seq Analysis Reveals the Progression of Human Osteoarthritis.” Journal Article. Ann Rheum Dis 78 (1): 100–110. https://doi.org/10.1136/annrheumdis-2017-212863.

Keren-Shaul, H., E. Kenigsberg, D. A. Jaitin, E. David, F. Paul, A. Tanay, and I. Amit. 2019. “MARS-Seq2.0: An Experimental and Analytical Pipeline for Indexed Sorting Combined with Single-Cell RNA Sequencing.” Journal Article. Nat Protoc 14 (6): 1841–62. https://doi.org/10.1038/s41596-019-0164-4.

Kowalczyk, M. S., I. Tirosh, D. Heckl, T. N. Rao, A. Dixit, B. J. Haas, R. K. Schneider, A. J. Wagers, B. L. Ebert, and A. Regev. 2015. “Single-Cell RNA-Seq Reveals Changes in Cell Cycle and Differentiation Programs Upon Aging of Hematopoietic Stem Cells.” Journal Article. Genome Res 25 (12): 1860–72. https://doi.org/10.1101/gr.192237.115.

Luecken, M. D., and F. J. Theis. 2019. “Current Best Practices in Single-Cell RNA-Seq Analysis: A Tutorial.” Journal Article. Mol Syst Biol 15 (6): e8746. https://doi.org/10.15252/msb.20188746.

Macosko, E. Z., A. Basu, R. Satija, J. Nemesh, K. Shekhar, M. Goldman, I. Tirosh, et al. 2015. “Highly Parallel Genome-Wide Expression Profiling of Individual Cells Using Nanoliter Droplets.” Journal Article. Cell 161 (5): 1202–14. https://doi.org/10.1016/j.cell.2015.05.002.

Majumdar, U., S. Manivannan, M. Basu, Y. Ueyama, M. C. Blaser, E. Cameron, M. R. McDermott, et al. 2021. “Nitric Oxide Prevents Aortic Valve Calcification by s-Nitrosylation of Usp9x to Activate NOTCH Signaling.” Journal Article. Sci Adv 7 (6). https://doi.org/10.1126/sciadv.abe3706.

Mathys, H., J. Davila-Velderrain, Z. Peng, F. Gao, S. Mohammadi, J. Z. Young, M. Menon, et al. 2019. “Single-Cell Transcriptomic Analysis of Alzheimer’s Disease.” Journal Article. Nature 570 (7761): 332–37. https://doi.org/10.1038/s41586-019-1195-2.

McCarthy, D. J., K. R. Campbell, A. T. Lun, and Q. F. Wills. 2017. “Scater: Pre-Processing, Quality Control, Normalization and Visualization of Single-Cell RNA-Seq Data in r.” Journal Article. Bioinformatics 33 (8): 1179–86. https://doi.org/10.1093/bioinformatics/btw777.

Mereu, E., A. Lafzi, C. Moutinho, C. Ziegenhain, D. J. McCarthy, A. Alvarez-Varela, E. Batlle, et al. 2020. “Benchmarking Single-Cell RNA-Sequencing Protocols for Cell Atlas Projects.” Journal Article. Nat Biotechnol 38 (6): 747–55. https://doi.org/10.1038/s41587-020-0469-4.

Nayak, R., and Y. Hasija. 2021. “A Hitchhiker’s Guide to Single-Cell Transcriptomics and Data Analysis Pipelines.” Journal Article. Genomics 113 (2): 606–19. https://doi.org/10.1016/j.ygeno.2021.01.007.

Osorio, D., and J. J. Cai. 2020. “Systematic Determination of the Mitochondrial Proportion in Human and Mice Tissues for Single-Cell RNA Sequencing Data Quality Control.” Journal Article. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa751.

Papalexi, E., and R. Satija. 2018. “Single-Cell RNA Sequencing to Explore Immune Cell Heterogeneity.” Journal Article. Nat Rev Immunol 18 (1): 35–45. https://doi.org/10.1038/nri.2017.76.

Picelli, S., O. R. Faridani, A. K. Bjorklund, G. Winberg, S. Sagasser, and R. Sandberg. 2014. “Full-Length RNA-Seq from Single Cells Using Smart-Seq2.” Journal Article. Nat Protoc 9 (1): 171–81. https://doi.org/10.1038/nprot.2014.006.

Polioudakis, D., L. de la Torre-Ubieta, J. Langerman, A. G. Elkins, X. Shi, J. L. Stein, C. K. Vuong, et al. 2019. “A Single-Cell Transcriptomic Atlas of Human Neocortical Development During Mid-Gestation.” Journal Article. Neuron 103 (5): 785–801 e8. https://doi.org/10.1016/j.neuron.2019.06.011.

Potter, S. S. 2018. “Single-Cell RNA Sequencing for the Study of Development, Physiology and Disease.” Journal Article. Nat Rev Nephrol 14 (8): 479–92. https://doi.org/10.1038/s41581-018-0021-7.

Qiu, X., A. Hill, J. Packer, D. Lin, Y. A. Ma, and C. Trapnell. 2017. “Single-Cell mRNA Quantification and Differential Analysis with Census.” Journal Article. Nat Methods 14 (3): 309–15. https://doi.org/10.1038/nmeth.4150.

Qiu, X., Q. Mao, Y. Tang, L. Wang, R. Chawla, H. A. Pliner, and C. Trapnell. 2017. “Reversed Graph Embedding Resolves Complex Single-Cell Trajectories.” Journal Article. Nat Methods 14 (10): 979–82. https://doi.org/10.1038/nmeth.4402.

Ravenscroft, T. A., J. Janssens, P. T. Lee, B. Tepe, P. C. Marcogliese, S. Makhzami, T. C. Holmes, S. Aerts, and H. J. Bellen. 2020. “Drosophila Voltage-Gated Sodium Channels Are Only Expressed in Active Neurons and Are Localized to Distal Axonal Initial Segment-Like Domains.” Journal Article. J Neurosci 40 (42): 7999–8024. https://doi.org/10.1523/JNEUROSCI.0142-20.2020.

Saliba, A. E., A. J. Westermann, S. A. Gorski, and J. Vogel. 2014. “Single-Cell RNA-Seq: Advances and Future Challenges.” Journal Article. Nucleic Acids Res 42 (14): 8845–60. https://doi.org/10.1093/nar/gku555.

Satija, R., J. A. Farrell, D. Gennert, A. F. Schier, and A. Regev. 2015. “Spatial Reconstruction of Single-Cell Gene Expression Data.” Journal Article. Nat Biotechnol 33 (5): 495–502. https://doi.org/10.1038/nbt.3192.

Shaw, R., X. Tian, and J. Xu. 2021. “Single-Cell Transcriptome Analysis in Plants: Advances and Challenges.” Journal Article. Mol Plant 14 (1): 115–26. https://doi.org/10.1016/j.molp.2020.10.012.

Soysa, T. Y. de, S. S. Ranade, S. Okawa, S. Ravichandran, Y. Huang, H. T. Salunga, A. Schricker, A. Del Sol, C. A. Gifford, and D. Srivastava. 2019. “Single-Cell Analysis of Cardiogenesis Reveals Basis for Organ-Level Developmental Defects.” Journal Article. Nature 572 (7767): 120–24. https://doi.org/10.1038/s41586-019-1414-x.

Stuart, T., A. Butler, P. Hoffman, C. Hafemeister, E. Papalexi, 3rd Mauck W. M., Y. Hao, M. Stoeckius, P. Smibert, and R. Satija. 2019. “Comprehensive Integration of Single-Cell Data.” Journal Article. Cell 177 (7): 1888–1902 e21. https://doi.org/10.1016/j.cell.2019.05.031.

Suva, M. L., and I. Tirosh. 2019. “Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges.” Journal Article. Mol Cell 75 (1): 7–12. https://doi.org/10.1016/j.molcel.2019.05.003.

Tang, F., C. Barbacioru, Y. Wang, E. Nordman, C. Lee, N. Xu, X. Wang, et al. 2009. “mRNA-Seq Whole-Transcriptome Analysis of a Single Cell.” Journal Article. Nat Methods 6 (5): 377–82. https://doi.org/10.1038/nmeth.1315.

Trapnell, C., D. Cacchiarelli, J. Grimsby, P. Pokharel, S. Li, M. Morse, N. J. Lennon, K. J. Livak, T. S. Mikkelsen, and J. L. Rinn. 2014. “The Dynamics and Regulators of Cell Fate Decisions Are Revealed by Pseudotemporal Ordering of Single Cells.” Journal Article. Nat Biotechnol 32 (4): 381–86. https://doi.org/10.1038/nbt.2859.

Vieth, B., S. Parekh, C. Ziegenhain, W. Enard, and I. Hellmann. 2019. “A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines.” Journal Article. Nat Commun 10 (1): 4667. https://doi.org/10.1038/s41467-019-12266-7.

Web Page. 2021a. https://www.illumina.com/content/dam/illumina-marketing/documents/products/other/single-cell-sequencing-ebook-770-2019-007.pdf.

———. 2021b. https://www.scrna-tools.org/.

———. n.d.a. https://satijalab.org/seurat/.

———. n.d.b. http://cole-trapnell-lab.github.io/monocle-release/docs/.

Wen, L., and F. Tang. 2016. “Single-Cell Sequencing in Stem Cell Biology.” Journal Article. Genome Biol 17: 71. https://doi.org/10.1186/s13059-016-0941-0.

Whitfield, M. L., G. Sherlock, A. J. Saldanha, J. I. Murray, C. A. Ball, K. E. Alexander, J. C. Matese, et al. 2002. “Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors.” Journal Article. Mol Biol Cell 13 (6): 1977–2000. https://doi.org/10.1091/mbc.02-02-0030.

Zhang, X., T. Li, F. Liu, Y. Chen, J. Yao, Z. Li, Y. Huang, and J. Wang. 2019. “Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems.” Journal Article. Mol Cell 73 (1): 130–142 e5. https://doi.org/10.1016/j.molcel.2018.10.020.

Zhang, Y., J. Gao, Y. Huang, and J. Wang. 2018. “Recent Developments in Single-Cell RNA-Seq of Microorganisms.” Journal Article. Biophys J 115 (2): 173–80. https://doi.org/10.1016/j.bpj.2018.06.008.

Zheng, G. X., J. M. Terry, P. Belgrader, P. Ryvkin, Z. W. Bent, R. Wilson, S. B. Ziraldo, et al. 2017. “Massively Parallel Digital Transcriptional Profiling of Single Cells.” Journal Article. Nat Commun 8: 14049. https://doi.org/10.1038/ncomms14049.