03-Nov-2020
prokaryotic cells has been hindered by their low levels of mRNA, lack of mRNA polyadenylation, and thick cell walls. Here, we present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a high-throughput prokaryotic scRNA-seq pipeline that overcomes these obstacles.
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the potential to greatly facilitate drug development. Boreström et al. have used CRISPR/Cas9 to create kidney ?uorescent lineage markers for SIX2 and NPHS1 to monitor the differentiation process to tubular and glomerular structures and optimize maturity. The convergence of “personalized” kidney organoids with genome editing and single-cell sequencing technology hold great promise to ...
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Immunity 53, 1–12, September 15, 2020 ª 2020 Elsevier Inc. 1 ll Please cite this article in press as: Zhu et al., Single-Cell Sequencing of Peripheral Mononuclear Cells Reveals Distinct Immune Response Landscapes
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Cell. 148, 886–895. Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Li F et al. 2012. Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloprolif-erative Neoplasm. Cell. 148, 873–885. Sample Requirements BGI single cell publications Single cell Few cells Cell line Whole blood Frozen tissue Total RNA for low input ...
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[email protected] (S.M.), [email protected] (D.A.H.) In Brief Circulating tumor cells (CTCs) are en- riched for the precursors of metastasis, but their composition has not been fully de?ned. Ting et al. have utilized a micro-?uidic device to perform single-cell RNA sequencing of pancreatic CTCs, identi-fying three distinct populations that sug-gest multiple paths ...
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DEPArray™ single cell isolaon (poster presented by Chudziak et al, and Chudziak et al, 2015) CTC 1 Molecular analysis of CTCs Background Individual CTCs, pools of CTCs and control WBCs were subjected to whole genome ampli?caon (WGA) and its e?cacy was evaluated by mul0plex PCR to determine the Genome Integrity Index (GII) of each sample Low pass whole genome sequencing (WGS) was used to
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Here we provide fundamental insights into early human development by single-cell RNA-sequencing of human and mouse preimplantation embryos. We elucidate conserved transcriptional programs along with those that are human-specific. Importantly, we validate our RNA-sequencing findings at the protein level, which further reveals differences in human and mouse embryo gene expression. For example ...
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mental samples is provided by single cell genomics and the generation of so-called ‘mini-metagenomes’, which couples the sorting of cells of interest from environmental samples with whole genome sequencing (Nurk et al., 2013; Kaster et al., 2014; Rinke et al. 2014). The information from genome analysis can then be applied to predict pathways and metabolism and design targeted isolation ...
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Molecular Cell Technology Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing Alba Rodriguez-Meira,1,2 Gemma Buck,1,2 Sally-Ann Clark,3 Benjamin J. Povinelli,1,2 Veronica Alcolea,1,2 Eleni Louka,1,2 Simon McGowan,4 Angela Hamblin,5 Nikolaos Sousos, 1 ,2Nikolaos Barkas, 1,2Alice Giustacchini, Bethan Psaila, 5 Sten Eirik W ...
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Unravelling biology and shifting paradigms in cancer with single-cell sequencing Timour Baslan and James Hicks Abstract | The fundamental operative unit of a cancer is the genetically and epigenetically innovative single cell. Whether proliferating or quiescent, in the primary tumour mass or disseminated elsewhere, single cells govern the parameters that dictate all facets of the biology of ...
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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 ...
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Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase ...
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critical molecular pathways in individual tumor cells and associated these pathways with therapeutic outcomes using patient-derived tumor xenografts (PDXs) [10, 11]. Stromal and innate immune cell components in PDXs may recapitulate the TME in human tumor tissues [24, 25], and species-specific analysis based on PDX models is one of the easiest ways to distinguish the TME (mouse transcriptome ...
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Defining endothelial cell functional heterogeneity and plasticity using single-cell RNA-sequencing The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Kalluri, Aditya Sreemadhav. 2019. Defining endothelial cell functional heterogeneity and plasticity using single ...
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To study antigen-specific T cell clonality, we have developed a method that allows selection of rare cells, based on RNA expression, before in-depth scRNA-seq (named SELECT-seq). We applied SELECT-seq to collect both TCR sequences and then transcriptomes from single cells of peripheral blood lym-phocytes activated by a Mycobacterium tuberculosis (Mtb) lysate. TCR sequence analysis allowed us ...
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Single-Cell Genomics: Approaches and Utility in Immunology Karlynn 2, E. Neu,1 Qingming Tang,2 Patrick C. Wilson,1 and Aly A. Khan * Single-cell genomics offers powerful tools for studying immune cells, which make it possible to observe rare and intermediate cell states that cannot be resolved at the population level. Advances in computer science and single-cell sequencing development ...
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Genetic Crosses and Quantitative Trait Analysis of Parasite and Host Phenotypes ... parasite evolution, population genetics, and drug resistances (37–44), leading to gen- eration of an updated reference P. falciparum genome with greatly improved annota-tion (45). More recently, single-cell sequencing techniques have begun to yield exciting information for mixed infections, genetic ...
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We first obtained human peri-implantation conceptuses by coculturing blastocysts with human primary EM cells (Fig 1A). Briefly, conceptuses generated by in vitro fertilization were first cultured to the blastocyst stage following the method described before by Shahbazi and colleagues and Deglincerti and colleagues [11, 12]. At the blastocyst stage (day 6.5), concep-tuses were transferred to ...
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Phage M13 is widely used in nucleotide sequencing and site-directedmutagenesissinceits genomecanexisteitherin a single-stranded form inside a phage coat or as a double-stranded replicative form within the infected cell. During replication, only the plus strand of the replicative form is selectively packaged bythe phage proteins (71). Therepli-
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15 – 21 Nov · EMBO Practical Course Single-Cell Omics 22 – 27 Nov · EMBO Practical Course Extracellular Vesicles: From Biology to Biomedical Applications 23 – 27 Nov · EMBL Course Next Generation Sequencing Bioinformatics 26 – 28 Nov EMBL Conference 22nd EMBL PhD Symposium DECEMBER 6 – 8 Dec · EMBO Workshop In situ Structural Biology – From Cryo-EM to Integrative Modelling 7 ...
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and quality of these methods have limited their widespread adoption. Here we describe a high-quality (105 nuclear fragments per cell) droplet-microfluidics-based method for single-cell profiling of chromatin accessibility. We use this approach, named ‘droplet single-cell assay for transposase-accessible chromatin using sequencing’ (dscATAC-seq), to assay 46,653 cells for the unbiased ...
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Topological Methods for Visualization and Analysis of High Dimensional Single-Cell RNA Sequencing Data Tongxin Wang Department of Computer Science, Indiana University Bloomington Bloomington, Indiana, 47408, USA Email: [email protected] Travis Johnson Department of Biomedical Informatics, Ohio State University Columbus, Ohio, 43210, USA Email: [email protected] Jie Zhang Department of Medical ...
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SYMPORTER 2 (SUC2) and TARGET OF MONOPTEROS 5 (TMO5)(De Rybel et al., 2014; Wu et al., 2016), root cap gene ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 33 (ANAC033)(Bennett et al., 2010), root hair gene COBRA-LIKE 9 (COBL9)(Kamiya et al., 2016), phloem gene PHLOEM PROTEIN 2-A1 (ATPP2-A1)(Cayla et al., 2015), endodermal gene MYB DOMAIN PROTEIN36 (MYB36) which promotes the development of casparian ...
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Article Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth Sarah Davidson,2,8 Mirjana Efremova,1,8 Angela Riedel,2 Bidesh Mahata,1,6 Jhuma Pramanik,1 Jani Huuhtanen,3 Gozde Kar, 1Roser Vento-Tormo, Tzachi Hagai,4 Xi Chen,1 Muzlifah A. Haniffa,5 Jacqueline D. Shields,2,8,9,* and Sarah A. Teichmann1,7,8,* 1Wellcome Sanger Institute, Wellcome Genome Campus ...
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APPLICATIONS OF SINGLE-CELL RNA-SEQ TO BASIC RESEARCH ... technical noise and biological variability for low-abundance transcripts loss of information •Study the transcriptome of whole organism: difficulties in maintaining the 3D information of tissue architecture at the same time as sequencing •Study of single-cell transcriptomics of prokaryotic cells: general lack of poly(A) tails in ...
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Key words: cell-free DNA, next-generation sequencing, methylation, cancer INTRODUCTION Earlier cancer detection offers the opportunity to identify tumors when cures are more achievable, outcomes are superior, and treatment can be less morbid.1,2 Effective screening paradigms exist only for a small subset of cancers, are focused on single cancer types, and have variable adoption and compliance ...
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Despite this, the global landscape of intercellular signaling in mammalian liver has not been eluci-dated. Here we perform single-cell RNA sequencing on non-parenchymal cells isolated from healthy and NASH mouse livers. Secretome gene analysis re-vealed a highly connected network of intrahepatic signaling and disruption of vascular signaling in NASH.We uncoveredtheemergence ofNASH-asso-ciated ...
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MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Finak, Greg, et al. "MAST: a flexible statistical framework for assessing transcriptional changes and characterizing ...
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Conclusion: We propose a collection of best practices to generate a highly detailed molecular cell atlas of highly informative frozen tissue stored in brain banks. Importantly, we have developed a new web application to make this unique single-nuclei molecular atlas publicly available.
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distribution Unimodal distribution Studying heterogeneity Lineage tracing study Stochastic gene expression X Liu S and TrapnellC. Single-cell transcriptome sequencing: recent advances and remaining challenges,F1000Research 2016(doi: 10.12688/f1000research.7223.1) Junker and van Oudenaarden; Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology, Cell 2014 (doi ...
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