Progress in Single Cell Sequencing Technology

Authors

  • Qicai Ma Northwest University For Nationalities
  • Wenli Wu
  • Na Ye
  • Xindong Wang
  • Ping Yan
  • Heping Pan

DOI:

https://doi.org/10.30564/jzr.v1i1.715

Abstract

Cells are the basic unit of life structure and life activities. Because of the complex micro-environment of cells, the content of components that play a key role is relatively small, so single-cell analysis is extremely challenging. In recent years, single-cell sequencing technology has been developed and matured. Single-cell sequencing can reveal the composition and physiological diversity of cells, and the existing single-cell separation technology, single-cell whole genome amplification technology, single The principles and applications of cell whole transcriptome amplification technology and single cell transcriptome sequencing are summarized and summarized.

Keywords:

Single cell isolation;Single cell sequencing;Whole genome;Transcriptome

References

[1] Liu Jia, Liu Zhen. Progress in single cell analysis [J]. Chromatography, 2016 (12).

[2] Bianconi E, Piovesan A, Facchin F, et al. An estimation of the number of cells in the human body.[J]. Annals of Human Biology, 2013, 40(6):463-471.

[3] Shirai M, Taniguchi T, Kambara H. Emerging Applications of Single-Cell Diagnostics[J]. Topics in Current Chemistry, 2014, 336:99.

[4] Zhu Zhongxu, Chen Xin. Progress in single cell sequencing technology and its application [J]. Genomics and Applied Biology, 2015, 34 (5): 000902-908.

[5] Nicholas N, James H. Future medical applications of single-cell sequencing in cancer[J]. Genome Medicine,3,5(2011-05-31), 2011, 3(5):31-31.

[6] Li Pin, He Ning, Li Yanming, et al. Progress in single-cell transcriptome data analysis and developmental biology[J]. Journal of Developmental Medicine, 2017(1).

[7] Dong Fang, Yuan Weiping, Cheng Tao. Application of Single Cell Technology in Stem Cell Research[J]. Chinese Journal of Cell Biology, 2013(1): 86-91.

[8] Chen Zixi, Chen Lei, Zhang Weiwen. Microbiology research at single cell scale: significance and method[J]. Acta Microbiologica Sinica, 2017(06):138-149.

[9] Li Xuping, Le Weidong. Application of Single Cell Gene Expression Analysis Technology in Neuroscience Research[J]. Progress in Physiological Sciences, 2006, 37(1): 55-57.

[10] Bull N D , Bartlett P F . The adult mouse hippocampal progenitor is neurogenic but not a stem cell.[J]. Journal of Neuroscience, 2005, 25(47):10815-10821.

[11] Ziegler A N , Schneider J S , Qin M , et al. IGF-II Promotes Stemness of Neural Restricted Precursors[J]. STEM CELLS, 2012, 30(6):0-0.

[12] Rota L M , Lazzarino D A , Ziegler A N , et al. Determini Mammosphere-Forming Potential: Application of the Limiting Dilution Analysis[J]. J Mammary Gland Biol Neoplasia, 2012, 17(2):119-123.

[13] Measuring gene expression in single bacterial cells: recent advances in methods and micro-devices[J]. Critical Reviews in Biotechnology, 2014, 35(4):1-13.

[14] Kirkness E F, Grindberg R V, Yee-Greenbaum J, et al. Sequencing of isolated sperm cells for direct haplotyping of a human genome[J]. Genome Research, 2013, 23(5):826-832.

[15] Navin N , Kendall J , Troge J , et al. Tumour evolution inferred by single-cell sequencing.[J]. Nature, 2011, 472(7341):90-94.

[16] Yilmaz S, Singh A K. Single cell genome sequencing.[J]. Current Opinion in Biotechnology, 2012, 23(3):437-443.

[17] Shapiro E, Biezuner T , Linnarsson S . Single-cell sequencing-based technologies will revolutionize whole-organism science.[J]. Nature Reviews Genetics, 2013, 14(9):618-30.

[18] Marcy Y , Ishoey T , Lasken R S , et al. Nanoliter reactors improve multiple displacement amplification of genomes from single cells.[J]. Plos Genetics, 2007, 3(9):1702-8.

[19] Streets A M , Zhang X , Cao C , et al. Microfluidic single-cell whole-transcriptome sequencing[J]. Proceedings of the National Academy of Sciences, 2014, 111(19):7048-7053.

[20] Whitesides G M. The origins and the future of microfluidics[J]. Nature, 2006, 442(7101):368-373.

[21] Squires T. Microfluidics: Fluid physics at the nanoliter scale[J]. Reviews of Modern Physics, 2005, 77(3):977-1026.

[22] Streets A M, Huang Y. Chip in a lab: Microfluidics for next generation life science research.[J]. Biomicrofluidics, 2013, 7(1):244-248.

[23] Bonner R F, Emmertbuck M, Cole K, et al. Laser capture microdissection: molecular analysis of tissue.[J]. Science, 1997, 278(5342):1481-1483.

[24] Frumkin D , Wasserstrom A , Itzkovitz S , et al. Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues.(Methodology article)(Technical report)[J]. Bmc Biotechnology, 2008, 8(1):1-16.

[25] Yilmaz S, Singh A K. Single cell genome sequencing.[J]. Current Opinion in Biotechnology, 2012, 23(3):437-443.

[26] Hu P , Zhang W , Xin H , et al. Single Cell Isolation and Analysis:[J].Frontiers in Cell & Developmental Biology, 2016, 4.

[27] Huang L, Ma F, Chapman A, et al. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications[J]. Annu Rev Genomics Hum Genet, 2015, 16(1):79-102.

[28] Guo H, Zhu P, Wu X, et al. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.[J]. Genome Research, 2013, 23(12):2126-2135.

[29] Li Y, Kim H J, Zheng C, et al. Primase-based whole genome amplification.[J]. Nucleic Acids Research, 2008, 36(13):e79-e79.

[30] Viguera E, Canceill D, Ehrlich S D. Replication slippage involves DNA polymerase pausing and dissociation[J]. Embo Journal, 2014, 20(10):2587-2595.

[31] Dean F B, Hosono S, Fang L, et al. Comprehensive human genome amplification using multiple displacement amplification.[J]. Proc Natl Acad Sci U S A, 2002, 99(8):5261-5266.

[32] Raghunathan A, Jr F H, Bornarth C J, et al. Genomic DNA amplification from a single bacterium[J]. Applied & Environmental Microbiology, 2005, 71(6):3342.

[33] Zong C, Xie X S. Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell[J]. Science, 2012, 338(6114):1622-6.

[34] Grün D, Vanoudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments[J]. Cell, 2015, 163(4):799-810.

[35] Lovett M. The applications of single-cell genomics[J]. Human Molecular Genetics, 2013, 22(1):R22-R26.

[36] Rothberg J M , Leamon J H . The development and impact of 454 sequencing[J]. Nature Biotechnology, 2008, 26(10):1117-24.

[37] Loman N J , Misra R V , Dallman T J , et al. Performance comparison of benchtop high-throughput sequencing platforms[J]. Nature Biotechnology, 2012, 30(5):434-439.

[38] Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high-density picolitre reactors.[J]. Nature, 2005.

[39] Bentley D R, Balasubramanian S, Swerdlow H P, et al. Accurate whole human genome sequencing using reversible terminator chemistry[J]. Nature, 2008.

[40] Ansorge W J. Next-generation DNA sequencing techniques.[J]. N Biotechnol, 2009, 25(4):195-203.

[41] Aird D, Ross M G, Chen W S, et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries[J]. Genome Biology, 2011, 12(2):R18-R18.

[42] Rothberg J M, Hinz W, Rearick T M, et al. An integrated semiconductor device enabling non-optical genome sequencing[J]. Nature, 2011, 475(7356):348.

[43] Robison K. Semiconductors charge into sequencing[J]. Nature Biotechnology, 2011, 29(9):805-7.

[44] Velculescu V E , Zhang L , Zhou W , et al. Characterization of the Yeast Transcriptome[J]. Cell, 1997, 88(2):243-251.

[45] Ping H , Wenhua Z , Hongbo X , et al. Single Cell Isolation and Analysis[J]. Frontiers in Cell and Developmental Biology, 2016, 4.

[46] Xue R , Li R , Bai F , et al. Single cell sequencing: technique, application,and future development[J]. Science Bulletin , 2015, 60(1):33.

[47] Tang F , Barbacioru C , Wang Y , et al. mRNA-Seq whole-transcriptome analysis of a single cell.[J]. Nature Methods, 2009, 6(5):377-382.

[48] Daniel Ramskold, Luo S , Wang Y C , et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells[J]. Nature Biotechnology, 2012, 30(8):777-782.

[49] Picelli S, Faridani O R, Bjorklund A K, et al. Full-length RNA-seq from single cells using Smart-seq2.[J]. Nature Protocols, 2014, 9(1):171-181.

[50] Islam S, Kjallquist U, Moliner A, et al. Characterization of the single-cell transcriptional landscape by highly multi-plex RNA-seq. Genome Res, 2011, 21(7): 1160-7

[51] Pan X, Durrett R E, Zhu H, et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells.[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(2):594-599.

[52] Pan X, Durrett R E, Zhu H, et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells.[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(2):594-599.

[53] Hashimshony T, Wagner F, Sher N, et al. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.[J]. Cell Reports, 2012, 2(3):666-673.

[54] Jaitin D A , Kenigsberg E , Kerenshaul H , et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.[J]. Science, 2014, 343(6172):776-779.

[55] Pan X, Durrett R E, Zhu H, et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells.[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(2):594-599.

[56] Liang Aibin, Liang Zhiyu, Wang Junbang. Single Cell Sequencing Technology and Its Application in Tumor Research[J]. Internal Medicine Theory and Practice, 2015(1): 18-22.

[57] Islam S, Kjällquist U, Moliner A, et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq[J]. Genome Research, 2011, 21(7):1160.

[58] Hashimshony T, Wagner F, Sher N, et al. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.[J]. Cell Reports, 2012, 2(3):666-673.

[59] White A K, Vaninsberghe M, Petriv O I, et al. High-throughput microfluidic single-cell RT-qPCR.[J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(34):13999-14004.

[60] Zhou Chaoping, Li Xinhui. Progress in Single Cell Transcriptome Research[J]. Progress in Biochemistry and Biophysics, 2013, 40(12): 1193-1200.

[61] Yan L, Yang M, Guo H, et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells[J]. Nature Structural & Molecular Biology, 2013, 20(9):1131.

Downloads

Issue

Article Type

Reviews