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single cell RNA sequencing,scRNA-seq

Yuval Lieberman, Lior Rokach, Tal Shay
Single-cell RNA sequencing (scRNA-seq) is an emerging technology for profiling the gene expression of thousands of cells at the single cell resolution. Currently, the labeling of cells in an scRNA-seq dataset is performed by manually characterizing clusters of cells or by fluorescence-activated cell sorting (FACS). Both methods have inherent drawbacks: The first depends on the clustering algorithm used and the knowledge and arbitrary decisions of the annotator, and the second involves an experimental step in addition to the sequencing and cannot be incorporated into the higher throughput scRNA-seq methods...
2018: PloS One
Eoghainín Ó hAinmhire, Haojia Wu, Yoshiharu Muto, Erinn L Donnelly, Flavia G Machado, Lucy X Fan, Monica Chang-Panesso, Benjamin D Humphreys
Gli1-positive resident mesenchymal stem cell-like cells are the predominant source of kidney myofibroblasts in fibrosis but investigating Gli1-positive myofibroblast progenitor activation is hampered by the difficulty of isolating and propagating primary cultures of these cells. Using a genetic strategy with positive and negative selection, we isolated Kidney-Gli1 (KG1) cells that maintain expression of appropriate mesenchymal stem cell-like cell markers, respond to hedgehog pathway activation and display robust myofibroblast differentiation upon treatment with TGFb...
October 10, 2018: American Journal of Physiology. Renal Physiology
Denis Avey, Sumithra Sankararaman, Aldrin K Y Yim, Ruteja Barve, Jeffrey Milbrandt, Robi D Mitra
Molecular and behavioral responses to opioids are thought to be primarily mediated by neurons, although there is accumulating evidence that other cell types play a prominent role in drug addiction. To investigate cell-type-specific opioid responses, we performed single-cell RNA sequencing (scRNA-seq) of the nucleus accumbens of mice following acute morphine treatment. Differential expression analysis uncovered unique morphine-dependent transcriptional responses by oligodendrocytes and astrocytes. We examined the expression of selected genes, including Cdkn1a and Sgk1, by FISH, confirming their induction by morphine in oligodendrocytes...
September 25, 2018: Cell Reports
Eun-Ah Christine Song, Sangwon Min, Akinsola Oyelakin, Kirsten Smalley, Jonathan E Bard, Lan Liao, Jianming Xu, Rose-Anne Romano
Stem and progenitor cells of the submandibular salivary gland (SMG) give rise to, maintain, and regenerate the multiple lineages of mature epithelial cells including those belonging to the ductal, acinar, basal and myoepithelial subtypes. Here we have exploited single cell RNA-sequencing and in vivo genetic lineage tracing technologies to generate a detailed map of the cell fate trajectories and branch points of the basal and myoepithelial cell populations of the mouse SMG during embryonic development and in adults...
September 19, 2018: Scientific Reports
Shelli F Farhadian, Sameet S Mehta, Chrysoula Zografou, Kevin Robertson, Richard W Price, Jenna Pappalardo, Jennifer Chiarella, David A Hafler, Serena S Spudich
Central nervous system (CNS) immune activation is an important driver of neuronal injury during several neurodegenerative and neuroinflammatory diseases. During HIV infection, CNS immune activation is associated with high rates of neurocognitive impairment, even during sustained long-term suppressive antiretroviral therapy (ART). However, the cellular subsets that drive immune activation and neuronal damage in the CNS during HIV infection and other neurological conditions remain unknown, in part because CNS cells are difficult to access in living humans...
September 20, 2018: JCI Insight
Saskia Freytag, Luyi Tian, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Background: The commercially available 10x Genomics protocol to generate droplet-based single-cell RNA-seq (scRNA-seq) data is enjoying growing popularity among researchers. Fundamental to the analysis of such scRNA-seq data is the ability to cluster similar or same cells into non-overlapping groups. Many competing methods have been proposed for this task, but there is currently little guidance with regards to which method to use. Methods: Here we use one gold standard 10x Genomics dataset, generated from the mixture of three cell lines, as well as three silver standard 10x Genomics datasets generated from peripheral blood mononuclear cells to examine not only the accuracy but also robustness of a dozen methods...
2018: F1000Research
Mihriban Karaayvaz, Simona Cristea, Shawn M Gillespie, Anoop P Patel, Ravindra Mylvaganam, Christina C Luo, Michelle C Specht, Bradley E Bernstein, Franziska Michor, Leif W Ellisen
Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. To investigate the underlying biology, we conducted single-cell RNA-sequencing (scRNA-seq) of >1500 cells from six primary TNBC. Here, we show that intercellular heterogeneity of gene expression programs within each tumor is variable and largely correlates with clonality of inferred genomic copy number changes, suggesting that genotype drives the gene expression phenotype of individual subpopulations...
September 4, 2018: Nature Communications
Mei Wang, Xixi Liu, Gang Chang, Yidong Chen, Geng An, Liying Yan, Shuai Gao, Yanwen Xu, Yueli Cui, Ji Dong, Yuhan Chen, Xiaoying Fan, Yuqiong Hu, Ke Song, Xiaohui Zhu, Yun Gao, Zhaokai Yao, Shuhui Bian, Yu Hou, Jiahao Lu, Rui Wang, Yong Fan, Ying Lian, Wenhao Tang, Yapeng Wang, Jianqiao Liu, Lianming Zhao, Luyu Wang, Zhaoting Liu, Renpei Yuan, Yujia Shi, Boqiang Hu, Xiulian Ren, Fuchou Tang, Xiao-Yang Zhao, Jie Qiao
Spermatogenesis generates mature male gametes and is critical for the proper transmission of genetic information between generations. However, the developmental landscapes of human spermatogenesis remain unknown. Here, we performed single-cell RNA sequencing (scRNA-seq) analysis for 2,854 testicular cells from donors with normal spermatogenesis and 174 testicular cells from one nonobstructive azoospermia (NOA) donor. A hierarchical model was established, which was characterized by the sequential and stepwise development of three spermatogonia subtypes, seven spermatocyte subtypes, and four spermatid subtypes...
October 4, 2018: Cell Stem Cell
Fengrui Wu, Yong Liu, Qingqing Wu, Dengkun Li, Ling Zhang, Xiaoqing Wu, Rong Wang, Di Zhang, Shaorong Gao, Wenyong Li
BACKGROUND: Long non-coding RNAs (lncRNAs), a type of epigenetic regulator, are thought to play important roles in embryonic development in mice, and several developmental defects are associated with epigenetic modification disorders. The most dramatic epigenetic reprogramming event occurs during somatic cell nuclear transfer (SCNT) when the expression profile of a differentiated cell is abolished, and a newly embryo-specific expression profile is established. However, the molecular mechanism underlying somatic reprogramming remains unclear, and the dynamics and functions of lncRNAs in this process have not yet been illustrated, resulting in inefficient reprogramming...
August 23, 2018: BMC Genomics
Taiyun Kim, Irene Rui Chen, Yingxin Lin, Andy Yi-Yang Wang, Jean Yee Hwa Yang, Pengyi Yang
Advances in high-throughput sequencing on single-cell gene expressions [single-cell RNA sequencing (scRNA-seq)] have enabled transcriptome profiling on individual cells from complex samples. A common goal in scRNA-seq data analysis is to discover and characterise cell types, typically through clustering methods. The quality of the clustering therefore plays a critical role in biological discovery. While numerous clustering algorithms have been proposed for scRNA-seq data, fundamentally they all rely on a similarity metric for categorising individual cells...
August 22, 2018: Briefings in Bioinformatics
Liqun He, Michael Vanlandewijck, Maarja Andaloussi Mäe, Johanna Andrae, Koji Ando, Francesca Del Gaudio, Khayrun Nahar, Thibaud Lebouvier, Bàrbara Laviña, Leonor Gouveia, Ying Sun, Elisabeth Raschperger, Åsa Segerstolpe, Jianping Liu, Sonja Gustafsson, Markus Räsänen, Yvette Zarb, Naoki Mochizuki, Annika Keller, Urban Lendahl, Christer Betsholtz
Vascular diseases are major causes of death, yet our understanding of the cellular constituents of blood vessels, including how differences in their gene expression profiles create diversity in vascular structure and function, is limited. In this paper, we describe a single-cell RNA sequencing (scRNA-seq) dataset that defines vascular and vessel-associated cell types and subtypes in mouse brain and lung. The dataset contains 3,436 single cell transcriptomes from mouse brain, which formed 15 distinct clusters corresponding to cell (sub)types, and another 1,504 single cell transcriptomes from mouse lung, which formed 17 cell clusters...
August 21, 2018: Scientific Data
Junil Kim, Diana E Stanescu, Kyoung Jae Won
Single-cell RNA sequencing (scRNA-seq) is a powerful tool to study heterogeneity and dynamic changes in cell populations. Clustering scRNA-seq is essential in identifying new cell types and studying their characteristics. We develop CellBIC (single Cell BImodal Clustering) to cluster scRNA-seq data based on modality in the gene expression distribution. Compared with classical bottom-up approaches that rely on a distance metric, CellBIC performs hierarchical clustering in a top-down manner. CellBIC outperformed the bottom-up hierarchical clustering approach and other recently developed clustering algorithms while maintaining the hierarchical structure of cells...
August 8, 2018: Nucleic Acids Research
Luyi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J Hilton, Shalin H Naik, Matthew E Ritchie
Single-cell RNA sequencing (scRNA-seq) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously. Protocols that incorporate both designed and random barcodes have greatly increased the throughput of scRNA-seq, but give rise to a more complex data structure. There is a need for new tools that can handle the various barcoding strategies used by different protocols and exploit this information for quality assessment at the sample-level and provide effective visualization of these results in preparation for higher-level analyses...
August 2018: PLoS Computational Biology
Byungjin Hwang, Ji Hyun Lee, Duhee Bang
Rapid progress in the development of next-generation sequencing (NGS) technologies in recent years has provided many valuable insights into complex biological systems, ranging from cancer genomics to diverse microbial communities. NGS-based technologies for genomics, transcriptomics, and epigenomics are now increasingly focused on the characterization of individual cells. These single-cell analyses will allow researchers to uncover new and potentially unexpected biological discoveries relative to traditional profiling methods that assess bulk populations...
August 7, 2018: Experimental & Molecular Medicine
Johannes W Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas E Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann, Wolfgang Enard
Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize cellular identities and processes. Consequently, improving its sensitivity, flexibility, and cost-efficiency can advance many research questions. Among the flexible plate-based methods, single-cell RNA barcoding and sequencing (SCRB-seq) is highly sensitive and efficient. Here, we systematically evaluate experimental conditions of this protocol and find that adding polyethylene glycol considerably increases sensitivity by enhancing cDNA synthesis...
July 26, 2018: Nature Communications
Quanbo Ji, Yuxuan Zheng, Guoqiang Zhang, Yuqiong Hu, Xiaoying Fan, Yu Hou, Lu Wen, Li Li, Yameng Xu, Yan Wang, Fuchou Tang
OBJECTIVES: Understanding the molecular mechanisms underlying human cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). Here, we report the molecular programmes and lineage progression patterns controlling human OA pathogenesis using single-cell RNA sequencing (scRNA-seq). METHODS: We performed unbiased transcriptome-wide scRNA-seq analysis, computational analysis and histological assays on 1464 chondrocytes from 10 patients with OA undergoing knee arthroplasty surgery...
July 19, 2018: Annals of the Rheumatic Diseases
Akira Nguyen, Weng Hua Khoo, Imogen Moran, Peter I Croucher, Tri Giang Phan
Single-cell RNA sequencing (scRNA-Seq) is transforming our ability to characterize cells, particularly rare cells that are often overlooked in bulk population analytical approaches. This has lead to the discovery of new cell types and cellular states that echo the underlying heterogeneity and plasticity in the immune system. Technologies for the capture, sequencing, and bioinformatic analysis of single cells are rapidly improving, and scRNA-Seq is now becoming much more accessible to non-specialized laboratories...
2018: Frontiers in Immunology
Di-Cheng Zhao, Yu-Mei Li, Jie-Liang Ma, Ning Yi, Zhong-Yuan Yao, Yan-Ping Li, Yi Quan, Xin-Ning Li, Chang-Long Xu, Ying Qiu, Ling-Qian Wu
Precise regulation of glucose metabolism-related genes is essential for early embryonic development. Although previous research has yielded detailed information on the biochemical processes, little is yet known of the dynamic gene expression profiles in glucose metabolism of preimplantation embryos at a single-cell resolution. In the present study, we performed integrated analysis of single-cell RNA sequencing (scRNA-seq) data of human preimplantation embryos that had been cultured in sequential medium. Different cells in the same embryo have similar gene expression patterns in glucose metabolism...
July 18, 2018: Reproduction, Fertility, and Development
Jinguo Chen, Foo Cheung, Rongye Shi, Huizhi Zhou, Wenrui Lu
BACKGROUND: Interest in single-cell transcriptomic analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. In almost all reported works investigators have used live cells, which introduces cell stress during preparation and hinders complex study designs. Recent studies have indicated that cells fixed by denaturing fixative can be used in single-cell sequencing, however they did not usually work with most types of primary cells including immune cells...
July 17, 2018: Journal of Translational Medicine
Lihua Zhang, Shihua Zhang
Single-cell RNA-sequencing (scRNA-seq) is a recent breakthrough technology, which paves the way for measuring RNA levels at single cell resolution to study precise biological functions. One of the main challenges when analyzing scRNA-seq data is the presence of zeros or dropout events, which may mislead downstream analyses. To compensate the dropout effect, several methods have been developed to impute gene expression since the first Bayesian-based method being proposed in 2016. However, these methods have shown very diverse characteristics in terms of model hypothesis and imputation performance...
June 19, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
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