Smart-seq2 for sensitive full-length transcriptome profiling in single cells

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5. A comprehensive library of human transcription factors for cell fate engineering
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6. A rapidly acting glutamatergic ARC→PVH satiety circuit postsynaptically regulated by α-MSH
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7. Single-cell RNA-sequencing: The future of genome biology is now
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8. Revolutionizing immunology with single-cell RNA sequencing
   Haide Chen, Fang Ye, Guoji Guo · 2019 · Cellular and Molecular Immunology
9. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells
   Vionnie W.C. Yu, Rushdia Zareen Yusuf, Toshihiko Oki, Juwell W. Wu, Borja Sáez, Xin Wang, Colleen Cook, Ninib Baryawno, Michael J. Ziller, Eunjung Lee et al. · 2017 · Cell
10. scSLAM-seq reveals core features of transcription dynamics in single cells
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11. Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor–directed therapies
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12. Fixed single-cell transcriptomic characterization of human radial glial diversity
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13. Single-cell transcriptome sequencing: recent advances and remaining challenges
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14. Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly
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15. High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery
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16. Prolonged epigenomic and synaptic plasticity alterations following single exposure to a psychedelic in mice
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17. Rare Pulmonary Neuroendocrine Cells Are Stem Cells Regulated by Rb, p53, and Notch
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18. Microfluidics-free single-cell genomics with templated emulsification
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19. Hypoxia Triggers the Intravasation of Clustered Circulating Tumor Cells
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20. A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians
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21. Genome-wide in vivo screen identifies novel host regulators of metastatic colonization
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22. A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate
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23. Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing
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24. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
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25. Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology
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26. Cell fixation and preservation for droplet-based single-cell transcriptomics
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27. Treg cells in health and autoimmune diseases: New insights from single cell analysis
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28. Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites
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29. Modeling gene regulatory networks using neural network architectures
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30. Characterization of directed differentiation by high-throughput single-cell RNA-Seq
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31. Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
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32. Single-cell sequencing of the small-RNA transcriptome
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33. Heterogeneity in immune responses: from populations to single cells
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34. Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma
    Grégory Seumois, Ciro Ramírez-Suástegui, Benjamin Joachim Schmiedel, Shu Ying Liang, Bjoern Peters, Alessandro Sette, Pandurangan Vijayanand · 2020 · Science Immunology
35. Atlas of the aging mouse brain reveals white matter as vulnerable foci
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36. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing
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37. Single-Cell (Multi)omics Technologies
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38. Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology
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39. Advances in single-cell RNA sequencing and its applications in cancer research
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40. Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella
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41. Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing
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42. APOE4 impairs the microglial response in Alzheimer’s disease by inducing TGFβ-mediated checkpoints
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43. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells
    Vionnie W.C. Yu, Rushdia Zareen Yusuf, Toshihiko Oki, Juwell W. Wu, Borja Sáez, Xin Wang, Colleen Cook, Ninib Baryawno, Michael J. Ziller, Eunjung Lee et al. · 2016 · Cell
44. Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
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45. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections
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46. Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation
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47. Single-cell sequencing in stem cell biology
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48. Introduction to Single‐Cell RNA Sequencing
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49. A systematic performance evaluation of clustering methods for single-cell RNA-seq data
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50. Restoring miR-132 expression rescues adult hippocampal neurogenesis and memory deficits in Alzheimer’s disease
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51. Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria
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52. Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells
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53. Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol
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54. A Single-Cell Sequencing Guide for Immunologists
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55. Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age
    Mann, Mati, Mehta, Arnav, de Boer, Carl G., Kowalczyk, Monika S., Lee, Kevin, Haldeman, Pearce, Rogel, Noga, Knecht, Abigail R., Farouq, Daneyal, Regev, Aviv et al. · 2018 · Cell Reports
56. A repeated molecular architecture across thalamic pathways
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57. Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain
    Jussi Kupari, Dmitry Usoskin, Marc Parisien, Daohua Lou, Yizhou Hu, Michael P. Fatt, Peter Lönnerberg, Mats Spångberg, Bengt Eriksson, Nikolaos Barkas et al. · 2021 · Nature Communications
58. Reversible De-differentiation of Mature White Adipocytes into Preadipocyte-like Precursors during Lactation
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59. Integrative analyses of single-cell transcriptome and regulome using MAESTRO
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60. Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells
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61. Transcriptional mediators of treatment resistance in lethal prostate cancer
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62. Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation
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63. A hypothalamus-habenula circuit controls aversion
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64. Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study
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65. Deep conservation of the enhancer regulatory code in animals
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66. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq
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67. scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells
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68. Position- and Hippo signaling-dependent plasticity during lineage segregation in the early mouse embryo
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69. Tracing the expression of circular RNAs in human pre-implantation embryos
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70. Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress
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71. Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq
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72. IL-15 activates mTOR and primes stress-activated gene expression leading to prolonged antitumor capacity of NK cells
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73. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity
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74. Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq
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75. Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes
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76. Altered neuronal migratory trajectories in human cerebral organoids derived from individuals with neuronal heterotopia
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77. Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis
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78. SCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data
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79. Disruption of the IL-33-ST2-AKT signaling axis impairs neurodevelopment by inhibiting microglial metabolic adaptation and phagocytic function
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80. Removal of batch effects using distribution-matching residual networks
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81. Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
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82. BNC1 deficiency-triggered ferroptosis through the NF2-YAP pathway induces primary ovarian insufficiency
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83. Fibroblasts: Immunomodulatory factors in refractory diabetic wound healing
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84. GABA Regulates Release of Inflammatory Cytokines From Peripheral Blood Mononuclear Cells and CD4+ T Cells and Is Immunosuppressive in Type 1 Diabetes
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85. Next-generation computational tools for interrogating cancer immunity
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86. New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data
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87. Single-cell transcriptome conservation in cryopreserved cells and tissues
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88. Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm
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89. Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology
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90. Early lineage segregation of multipotent embryonic mammary gland progenitors
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91. The miR172/ IDS1 signaling module confers salt tolerance through maintaining ROS homeostasis in cereal crops
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92. Transcriptional profiling of mouse peripheral nerves to the single-cell level to build a sciatic nerve ATlas (SNAT)
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93. Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
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94. Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells
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95. A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
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96. Molecular transitions in early progenitors during human cord blood hematopoiesis
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97. Single-Cell RNA Sequencing Resolves Spatiotemporal Development of Pre-thymic Lymphoid Progenitors and Thymus Organogenesis in Human Embryos
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98. Neuropilin-1 is a T cell memory checkpoint limiting long-term antitumor immunity
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99. Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST
    Zhi‐Jie Cao, Wei Lin, Lu Shen, De-Chang Yang, Ge Gao · 2020 · Nature Communications
100. High-throughput single-сell sequencing in cancer research
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