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Single-Cell Research an Overview of Recent Single-Cell Research Publications Featuring Illumina® Technology

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Single-Cell Research An Overview of Recent Single-Cell Research Publications Featuring Illumina® Technology TABLE OF CONTENTS 5 Introduction Multiple Annealing and Looping–Based Amplification Cycles 7 Applications Genomic DNA and mRNA Sequencing Cancer 68 Epigenomics Methods Metagenomics Single-Cell Assay for Transposase- Stem Cells Accessible Chromatin Using Developmental Biology Sequencing Immunology Single-Cell Bisulfite Sequencing/ Neurobiology Single-Cell Whole-Genome Bisulfite Sequencing Drug Discovery Single-Cell Methylome & Transcriptome Reproductive Health Sequencing Microbial Ecology and Evolution Single-Cell Reduced-Representation Plant Biology Bisulfite Sequencing Forensics Single-Cell Chromatin Allele-Specific Gene Expression Immunoprecipitation Sequencing Chromatin Conformation Capture 50 Sample Preparation Sequencing Droplet-Based Chromatin 54 Data Analysis Immunoprecipitation Sequencing 60 DNA Methods 78 RNA Methods Multiple-Strand Displacement Designed Primer–Based RNA Amplification Sequencing Genome & Transcriptome Sequencing Single-Cell Universal Poly(A)- Independent RNA Sequencing For Research Use Only. Not for use in diagnostic procedures. An overview of recent publications featuring Illumina tecnology 3 Quartz-Seq Smart-Seq Smart-Seq2 Single-Cell Methylome & Transcriptome Sequencing Genome & Transcriptome Sequencing Genomic DNA and mRNA Sequencing T Cell–Receptor Chain Pairing Unique Molecular Identifiers Cell Expression by Linear Amplification Sequencing Flow Cell–Surface Reverse-Transcription Sequencing Single-Cell Tagged Reverse- Transcription Sequencing Fixed and Recovered Intact Single-Cell RNA Sequencing Cell Labeling via Photobleaching Indexing Droplets Drop-Seq CytoSeq Single-Cell RNA Barcoding and Sequencing High-Throughput Single-Cell Labeling For Research Use Only. Not for use in diagnostic procedures. 4 Single-cell Research INTRODUCTION Living tissues are composed of a variety of cell types. Each cell type has a distinct 1. Tanay A and Regev A. Scaling single-cell lineage and unique function that contribute to tissue and organ biology and, ultimately, genomics from phenomenology to mechanism. define the biology of the organism as a whole. The lineage and development stage of Nature. 2017;541:331-338 2. Regev A, Teichmann SA, Lander ES, et al. The each cell determine how they respond to other cells and to their native environment. Human Cell Atlas. Elife. 2017;6: e27041 In addition, subpopulations of cells of the same type are often genetically heterogeneous 3. Zhang X, Marjani SL, Hu Z, Weissman SM, Pan 1 X and Wu S. Single-Cell Sequencing for Precise from each other as well as from other cell types. Recently, scientists have launched Cancer Research: Progress and Prospects. the ambitious Human Cell Atlas Project, an international collaborative effort to map all Cancer Res. 2016;76:1305-1312 4. Wang Y and Navin NE. Advances and applica- 2 cell types in the human body by using single-cell sequencing. tions of single-cell sequencing technologies. Mol Cell. 2015;58:598-609 5. Solden L, Lloyd K and Wrighton K. The bright “Single-cell sequencing has emerged as a side of microbial dark matter: lessons learned from the uncultivated majority. Curr Opin Micro- revolutionary method that reveals biological processes biol. 2016;31:217-226 with unprecedented resolution and scale, and has 6. Bergholz TM, Moreno Switt AI and Wiedmann M. Omics approaches in food safety: fulfilling already greatly impacted biology and medicine.” the promise? Trends Microbiol. 2014;22:275- 281 - Benitez et al. 2017 7. Woyke T, Doud DFR and Schulz F. The trajec- tory of microbial single-cell sequencing. Nat Much of the initial impetus for single-cell tissue sequencing has come from cancer Methods. 2017;14:1045-1054 8. Mills E and Avraham R. Breaking the popula- research, where cell lineage and detection of residual disease is of paramount tion barrier by single cell analysis: one host importance.3 Currently, single-cell approaches are also used to improve our against one pathogen. Curr Opin Microbiol. 2017;36:69-75 understanding of other complex biological systems, including the central nervous 9. Hug LA, Baker BJ, Anantharaman K, et al. A system (CNS), immune system, and mammalian development.4 new view of the tree of life. Nature Microbiol- ogy. 2016;1:16048 10. Bacher R and Kendziorski C. Design and com- putational analysis of single-cell RNA-sequenc- Single-cell sequencing is also an effective approach to characterize organisms that ing experiments. Genome Biol. 2016;17:63 are difficult to culture in vitro.5 Advances in single-cell sequencing have improved the 11. Macosko EZ, Basu A, Satija R, et al. Highly Parallel Genome-wide Expression Profiling of detection and analysis of infectious diseases, food-borne pathogens, and microbial Individual Cells Using Nanoliter Droplets. Cell. diversities in the environment or the gut. 6,7,8,9 2015;161:1202-1214 12. Klein AM, Mazutis L, Akartuna I, et al. Droplet barcoding for single-cell transcriptomics The high accuracy and specificity of next-generation sequencing (NGS) makes it applied to embryonic stem cells. Cell. 2015;161:1187-1201 ideal for single-cell and low-level DNA/RNA sequencing. The growing collection of 13. Lee JH, Daugharthy ER, Scheiman J, et al. published single-cell techniques includes detection of DNA mutations, copy-number Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells variants (CNVs), DNA-protein binding, RNA splicing, and the measurement of mRNA and tissues. Nat Protoc. 2015;10:442-458 expression.10 More recently, microfluidics platforms and droplet-based methods 14. Lovatt D, Ruble BK, Lee J, et al. Transcriptome in vivo analysis (TIVA) of spatially defined single have enabled massively parallel sequencing of mRNA in large numbers of individual cells in live tissue. Nat Methods. 2014;11:190- 196 11,12 cells. The function of an individual cell is largely governed by interactions with its 15. Satija R, Farrell JA, Gennert D, Schier AF and neighbors. This spatial context is typically lost in single-cell sequencing experiments, Regev A. Spatial reconstruction of single- cell gene expression data. Nat Biotechnol. but new methods13,14 and analysis algorithms15 are combining measurements of 2015;33:495-502 single-cell gene expression with spatial localization within tissues. This review highlights recent publications demonstrating how Illumina technology is being used in single-cell sequencing applications and techniques. To learn more about Illumina sequencing and microarray technologies, visit www.illumina.com. For Research Use Only. Not for use in diagnostic procedures. An overview of recent publications featuring Illumina tecnology 5 The same gene can be expressed at different levels, and influenced by different control mechanisms, in different cell types within the same tissue. Reviews Baslan T and Hicks J. Unravelling biology and shifting paradigms in cancer with single-cell sequencing. Nat Rev Cancer. 2017;17:557-569 Benitez JA, Cheng S and Deng Q. Revealing allele-specific gene expression by single-cell transcriptomics. Int J Biochem Cell Biol. 2017;90:155-160 Haque A, Engel J, Teichmann SA and Lonnberg T. A practical guide to single-cell RNA-sequencing for bio- medical research and clinical applications. Genome Med. 2017;9:75 Marioni JC and Arendt D. How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology. Annu Rev Cell Dev Biol. 2017;33:537-553 Tanay A and Regev A. Scaling single-cell genomics from phenomenology to mechanism. Nature. 2017;541:331-338 Gawad C, Koh W and Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet. 2016;17:175-188 Liu S and Trapnell C. Single-cell transcriptome sequencing: recent advances and remaining challenges [version 1; referees: 2 approved]. F1000Research. 2016;5(F1000 Faculty Review):182 Grun D and van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015;163:799-810 Wang Y and Navin NE. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58:598-609 For Research Use Only. Not for use in diagnostic procedures. 6 Single-cell Research APPLICATIONS Cancer 16. Ellsworth DL, Blackburn HL, Shriver CD, Rabizadeh S, Soon-Shiong P and Ellsworth Tumor progression occurs through driver mutations that undergo Darwinian selection RE. Single-cell sequencing and tumorigenesis: improved understanding of tumor evolution for successive clonal expansion of tumor subclones. As a result, advanced tumors and metastasis. Clin Transl Med. 2017;6:15 may contain a number of unique subclones16,17,18 with different sets of mutations, 17. Baslan T and Hicks J. Unravelling biology and shifting paradigms in cancer with single-cell 19, 20,21 different histopathology, and different responses to therapy. Molecular profiling sequencing. Nat Rev Cancer. 2017;17:557- of all subclones at diagnosis is important, because a subclone that makes up only 569 18. Litzenburger UM, Buenrostro JD, Wu B, et 22 0.3% of a primary tumor can become the predominant clone following relapse. al. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol. Deep sequencing can detect subclone abundance as low as 1% of the total 2017;18:15 tumor cell population, but single-cell sequencing approaches are required to fully 19. Li H, Courtois ET, Sengupta D, et al. Refer- 23,24 ence component analysis of single-cell characterize therapeutic efficacy on rare cell populations. transcriptomes elucidates
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