Abstract
Research on the hierarchical nature of cell differentiation and heterogeneity in tissues has been performed by isolating and identifying cells by the use of monoclonal antibodies, cell sorting, microdissection, and functional assays. However, it is difficult to analyze continuous changes in cell differentiation and the identification of cells for which cell markers are unclear. Furthermore, cell populations considered identical were shown to be diverse. Recently, single cell gene expression analysis was performed to help understand the complexity of cell populations. Single-cell analysis can analyze the diversity of individual cell populations as well as the tissue microenvironment, and is extremely useful for research on intercellular interactions in diseases and identifying specific marker genes. Recent advances in technology have made it possible to analyze hundreds of single cells. In this paper, we introduce our newly developed well-based single-cell transcriptome method, which includes other methods.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Buettner F, et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol. 2015;33:155–60. https://doi.org/10.1038/nbt.3102.
Fan X, et al. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 2015a;16:148. https://doi.org/10.1186/s13059-015-0706-1.
Fan HC, Fu GK, Fodor SP. Expression profiling. Combinatorial labeling of single cells for gene expression cytometry. Science. 2015b;347(6222):1258367.
Gierahn TM, et al. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods. 2017;14:395–8. https://doi.org/10.1038/nmeth.4179.
Han X, et al. Mapping the mouse cell atlas by microwell-seq. Cell. 2018;172:1091–1107.e17. https://doi.org/10.1016/j.cell.
Hashimoto S, et al. Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues. Sci Rep. 2017;7:14225. https://doi.org/10.1038/s41598-017-14676-3.
Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2012;2:666–73. https://doi.org/10.1016/j.celrep.2012.08.003.
Jaitin DA, et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science. 2014;343:776–9. https://doi.org/10.1126/science.1247651.
Klein AM, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 2015;161:1187–201. https://doi.org/10.1016/j.cell.2015.04.044.
Li WV, Li JJ. An accurate and robust imputation method scImpute for single-cell RNA-seq data. Nat Commun. 2018;9:997. https://doi.org/10.1038/s41467-018-03405-7.
Macosko EZ, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161:1202–14. https://doi.org/10.1016/j.cell.2015.05.002.
Patel AP, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014;344:1396–401. https://doi.org/10.1126/science.1254257.
Picelli S, et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 2014;9:171–81. https://doi.org/10.1038/nprot.2014.006.
Pollen AA, et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol. 2014;32:1053–8. https://doi.org/10.1038/nbt.2967.
Sasagawa Y, et al. Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol. 2013;14:R31. https://doi.org/10.1186/gb-2013-14-4-r31.
Treutlein B, et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature. 2014;509:371–5. https://doi.org/10.1038/nature13173.
Acknowledgements
We are most grateful to T Torigoe, Y Hirohashi and Y Takamura for technical assistance. This research is (partially) supported by JST CREST Grant Number JPMJCR15G3, Japan, and Japan Agency for Medical Research and Development (AMED).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Hashimoto, S. (2019). Nx1-Seq (Well Based Single-Cell Analysis System). In: Suzuki, Y. (eds) Single Molecule and Single Cell Sequencing. Advances in Experimental Medicine and Biology, vol 1129. Springer, Singapore. https://doi.org/10.1007/978-981-13-6037-4_4
Download citation
DOI: https://doi.org/10.1007/978-981-13-6037-4_4
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-6036-7
Online ISBN: 978-981-13-6037-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)