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Search · four archives
26 papers · ranked by Valyu relevance
Grace X.Y. Zheng, Jessica M. Terry, Phillip Belgrader, Paul Ryvkin + 28 more
Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of up to tens of thousands of single cells per sample. Cell encapsulation in droplets takes place in ∼6 minutes, with ∼50% cell capture…
Serena Liu, Cole Trapnell
Single-cell RNA-sequencing methods are now robust and economically practical and are becoming a powerful tool for high-throughput, high-resolution transcriptomic analysis of cell states and dynamics. Single-cell approaches circumvent the averaging artifacts associated with traditional bulk population data, yielding new…
Laura Mincarelli, Ashleigh Lister, James Lipscombe, Iain C. Macaulay
Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different…
Junyue Cao, Jonathan S. Packer, Vijay Ramani, Darren A. Cusanovich + 10 more
Conventional methods for profiling the molecular content of biological samples fail to resolve heterogeneity that is present at the level of single cells. In the past few years, single cell RNA sequencing has emerged as a powerful strategy for overcoming this challenge. However, its adoption has been limited by a…
Getnet Molla Desta, Alemayehu Godana Birhanu
In recent years, significant advancements in biochemistry, materials science, engineering, and computer-aided testing have driven the development of high-throughput tools for profiling genetic information. Single-cell RNA sequencing (scRNA-seq) technologies have established themselves as key tools for dissecting…
Leland B. Hyman, Clare R. Christopher, Philip A. Romero
Experimental methods that capture the individual properties of single cells are revealing the key role of cell-to-cell variability in countless biological processes. These single-cell methods are becoming increasingly important across the life sciences in fields such as immunology, regenerative medicine, and cancer…
Karen Davey, Daniel Wong, Filip Konopacki, Eugene Kwa + 2 more
Single cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3’ mRNA capture of ∼50,000 single…
Jian Wang, Yuanlin Song
Single cell sequencing (SCS) has become a new approach to study biological heterogeneity. The advancement in technologies for single cell isolation, amplification of genome/transcriptome and next-generation sequencing enables SCS to reveal the inherent properties of a single cell from the large scale of the genome…
Itamar Kanter, Tomer Kalisky
Traditionally, gene expression measurements were performed on “bulk” samples containing populations of thousands of cells. Recent advances in genomic technology have made it possible to measure gene expression in hundreds of individual cells at a time. As a result, cellular properties that were previously masked in…
H. Robert Frost
Single cell RNA sequencing (scRNA-seq) is a powerful tool for analyzing complex tissues with recent advances enabling the transcriptomic profiling of thousands to tens-of-thousands of individual cells. Although scRNA-seq provides unprecedented insights into the biology of heterogeneous cell populations, analyzing such…
Paulina M. Strzelecka, Anna M. Ranzoni, Ana Cvejic
Probing cellular population diversity at single-cell resolution became possible only in recent years. The popularity of single-cell ‘omic’ approaches, which allow researchers to dissect sample heterogeneity and cell-to-cell variation, continues to grow. With continuous technological improvements, single-cell omics are…
Xinghua Pan
Single-cell analysis heralds a new era that allows “omics” analysis, notably genomics, transcriptomics, epigenomics and proteomics at the single-cell level. It enables the identification of the minor subpopulations that may play a critical role in a biological process of a population of cells, which conventionally are…
P. Marafini, DG. Smith, AR. Lamstaes, RE. Contreras + 22 more
Existing tools for single cell genomics require complex physical frameworks for the indexing of cellular nucleic acids, including proprietary instrumentation, droplet emulsions, and laborious combinatorial indexing schemes. The complexity and cost of these tools significantly constrains the use of single cell…
Kayleigh Casmey, Maria Zimmermann, Yuxin Xie, Sierra A. Codeluppi-Arrowsmith + 2 more
Single-cell omics technology has advanced rapidly since its inception, offering increasing precision, resolution, and technical diversity to explore cell-specific molecular features in the human brain and neuropsychiatric disorders. While traditional bulk genomic analyses have provided valuable insights into the…
Dylan Molho, Jiayuan Ding, Zhaoheng Li, Hongzhi Wen + 11 more
'Yixin Wang' 'Julian Venegas' 'Wei Jin' 'Renming Liu' 'Runze Su' 'Patrick Danaher' 'Robert Yang' 'Yu L. Lei' 'Yuying Xie' 'Jiliang Tang'] Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous…
Allen W. Zhang, Kieran R. Campbell
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays offer new insights into tumour heterogeneity, which underlies cancer initiation…
Shi-Xiong Zhang, Xiangtao Li, Qiuzhen Lin, Ka‐Chun Wong
In this study, we review the existing single-cell RNA-seq data clustering methods with critical insights into the related advantages and limitations. In addition, we also review the upstream singlecell RNA-seq data processing techniques such as quality control, normalization, and dimension reduction. We conduct…
Kerem Wainer-Katsir, Michal Linial
Current technologies for single-cell transcriptomics allow thousands of cells to be analyzed in a single experiment. The increased scale of these methods led to a higher risk of cell doublets’ contamination. Available tools and algorithms for identifying doublets and estimating their occurrence in single-cell…
Jafar Isbarov, Elmir Mahammadov
analysis Authors: ['Jafar Isbarov' 'Elmir Mahammadov'] Single-cell analysis is an increasingly relevant approach in "omics" studies. In the last decade, it has been applied to various fields, including cancer biology, neuroscience, and, especially, developmental biology. This rise in popularity has been accompanied…
Shuang Ge, Shuqing Sun, Huan Xu, Qiang Cheng + 1 more
Advances and Challenges from a Data Science Perspective Authors: ['Shuang Ge' 'Shuqing Sun' 'Huan Xu' 'Qiang Cheng' 'Zhixiang Ren'] The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial…
Hyeongseon Jeon, Juan Xie, Yeseul Jeon, Kyeong Joo Jung + 3 more
'Arkobrato Gupta' 'Won Chang' 'Dongjun Chung'] Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…
Authors not listed
Single-cell mass spectrometry (SCMS) has emerged as a powerful tool for analyzing metabolites in individual cells, including live cells. However, cell metabolites have rapid turnover rate, whereas maintaining metabolites’ profiles of live cells during sample transport, storage, or extended measurements can be…
Authors not listed
Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) is a powerful technique for molecular analysis of surfaces; however, its application of single cell studies has not been previously published. In the current work, a commercial DESI setup (DESI XS) coupled to a mass spectrometer was used to analyze…
Authors not listed
The WRN helicase has recently emerged as a promising therapeutic target for microsatellite instability (MSI)-high cancers. Here, we report LXW-P1, a potent WRN degrader derived from marine bromotyrosine alkaloids. Its molecular target was identified using an AI-guided, pathway-informed perturbation transcriptomics…
Authors not listed
The Single-probe is a multifunctional device that can be coupled to mass spectrometry (MS) for molecular analysis of microscale samples, such as single cells, tissue slices, and multicellular spheroids, under ambient conditions. In Single-probe single cell MS (SCMS) studies, this technique leverages direct sampling and…