摘要Single-cell sequencing is a powerful tool for delineating clonal relationship and identifying key driver genes for personalized cancer management. Here we performed single-cell sequencing analysis of a case of colon cancer. Population genetics analyses identified two independent clones in tumor cell population. The major tumor clone harbored APC and TP53 mutations as early oncogenic events, whereas the minor clone contained preponderant CDC27 and PABPC1 mutations. The absence of APC and TP53 mutations in the minor clone supports that these two clones were derived from two cellular origins. Examination of somatic mutation allele frequency spectra of additional 21 whole-tissue exome-sequenced cases revealed the heterogeneity of clonal origins in colon cancer. Next, we identified a mutated gene SLC12A5 that showed a high frequency of mutation at the single-cell level but exhibited low prevalence at the population level. Functional characterization of mutant SLC12A5 revealed its potential ...

North America Single Cell Analysis Market Forecast 2017-2025 North America Single Cell Analysis Market Forecast 2017-2025 KEY FINDINGS North America Single cell analysis market collected a revenue - Market research report and industry analysis - 10914389

This study aims to develop droplet-based microfluidics for massively parallel single-cell genomics, to elucidate intra-tissue genetic heterogeneity at the single-cell resolution. Most tumors display extensive intra-tumor heterogeneity, with various subpopulations of cells contains different mutations. For understanding these intra-tissue heterogeneities, ideal single-cell genomics methods should analyze tens of thousands of single cells in an efficient manner. In this study, I will develop droplet-based microfluidic techniques to produce the compartmentalized reaction environments for single-cell sequencing.. ...

CD Genomics provides comprehensive Single-Cell sequencing services to study Single-Cell genomics， which helps to uncover cell lineage relationships.

TY - JOUR. T1 - Single-cell gene expression profiling using FACS and qPCR with internal standards. AU - Porter, Joshua R.. AU - Telford, William G.. AU - Batchelor, Eric. N1 - Funding Information: We would like to thank V. Kapoor in the CCR ETIB Flow Cytometry Core for her aid in performing the cell sorting during the development of this protocol. We also thank M. Raffeld and the CCR LP Molecular Diagnostics Unit and J. Zhu and the NHLBI DNA Sequencing and Genomics Core for their aid in performing the qPCR during the development of this protocol. This research was supported by the Intramural Program of the NIH.. PY - 2017/2/25. Y1 - 2017/2/25. N2 - Gene expression measurements from bulk populations of cells can obscure the considerable transcriptomic variation of individual cells within those populations. Single-cell gene expression measurements can help assess the role of noise in gene expression, identify correlations in the expression of pairs of genes, and reveal subpopulations of cells that ...

Since different chromosomes showed varying degrees of gain or loss in the T-ALLs (Fig. 3d-h and Additional file 9: Figure S6b, c), we wondered whether calculating the aneuploidy and heterogeneity scores for individual chromosomes would reveal whether specific chromosomes more often showed changes in copy number than others. To this end, we plotted both scores per chromosome for all samples that were analysed by single-cell sequencing. For the control thymus, all chromosomes clustered together in the bottom left, indicating that none of the cells displayed chromosome copy number alterations (Fig. 4b, control thymus). In contrast, in the tumours we identified three types of chromosomes: (1) chromosomes that were (virtually) never lost or gained (Fig. 4b, green chromosomes in T260 and T158), presumably due to lethality associated with such gain/loss events; (2) chromosomes that show a high heterogeneity rate, but low aneuploidy rate, for which copy number changes are presumably not selected for ...

Author: Winkel, Matthias et al.; Genre: Journal Article; Published in Print: 2016-06-21; Open Access; Title: Single-cell sequencing of Thiomargarita reveals genomic flexibility for adaptation to dynamic redox conditions

Using single-cell sequencing and an in vitro culture system, researchers followed transcriptomic and epigenomic features over time in three main embryonic cell lineages.

It turns out that sequencing individual genomes in a population reveals a rich tapestry of variation that is lost when analyzing the average of DNA pooled from larger cell numbers. Kun Zhang, Mike McConnell and Xuyu Cai (Christopher Walsh lab) have been applying single-cell genome sequencing to neuronal cells, finding that a subset of cells can often harbor mutations not seen elsewhere in the brain, creating a patchwork of genotypes. The Single Cell Analyses meeting took place at the same time as The Scripps Institutes Future of Genomic Medicine conference, which focuses on the field of personal genomes. The mosaicism revealed by single-cell genome sequencing serves as an important reminder that each person has not one personal genome, but many.. Perhaps the best known application of single-cell genome sequencing is the tracking of tumor evolution, where the power of single-cell analyses is leveraged against the known genomic instability, and hence within-individual variability, of cancer ...

Characterizing the complex composition of solid tumors is fundamental for understanding tumor initiation, progression and metastasis. While patient-derived samples provide valuable insight, they are heterogeneous on multiple molecular levels, and often originate from advanced tumor stages. Here, we use single-cell transcriptome and epitope profiling together with pathway and lineage analyses to study tumorigenesis from a developmental perspective in a mouse model of salivary gland squamous cell carcinoma. We provide a comprehensive cell atlas and characterize tumor-specific cells. We find that these cells are connected along a reproducible developmental trajectory: initiated in basal cells exhibiting an epithelial-to-mesenchymal transition signature, tumorigenesis proceeds through Wnt-differential cancer stem cell-like subpopulations before differentiating into luminal-like cells. Our work provides unbiased insights into tumor-specific cellular identities in a whole tissue environment, and ...

Single-cell RNA-seq reveals the cellular heterogeneity inherent in the population of cells, which is very important in many clinical and research applications. Recent advances in droplet microfluidics have achieved the automatic isolation, lysis, and labeling of single cells in droplet compartments without complex Droplet-based single-cell sequencing

The ability to manipulate and selectively localize cells into patterns or distinct microenvironments is critical for single cell analysis [1-4], tissue engineering [5, 6], cell signaling studies [7-9], drug screening [10-12], and cell migration assays [13, 14]. Exploring the population dynamics and communal contributions within heterogeneous cell populations is fundamental to furthering our understanding of disease pathology [15-18]. In recent years, much effort has been focused on developing innovative, active and passive cell patterning methods and applications thereof. Many active cell patterning and isolation methods utilize microfluidic systems, in which cells are manipulated and transported using fluidic forces. Inkjet-based cell printing and deposition methods have proven effective at sorting and patterning cells at the bulk and single cell level, but are typically low throughput and raise concerns about cell stress responses [19-22]. A variety of microfluidic geometries have been used ...

Every cell is unique. QIAGENs solutions accelerate single cell analysis in diverse research areas, from oncology, immunology and microbiology to neuroscience, stem cell and developmental biology, allowing you to access the smallest dimensions of biological research. Decipher the genomic and transcriptomic differences between cells and uncover the heterogeneity in your sample for new biological insights. Enter the world of the single cell through this dedicated resource site and explore single cell applications and discover products that best match your needs. Take advantage of our extensive knowledge hub to access informative resources including webinars, posters, videos and scientific publications. ...

Every cell is unique. QIAGENs solutions accelerate single cell analysis in diverse research areas, from oncology, immunology and microbiology to neuroscience, stem cell and developmental biology, allowing you to access the smallest dimensions of biological research. Decipher the genomic and transcriptomic differences between cells and uncover the heterogeneity in your sample for new biological insights. Enter the world of the single cell through this dedicated resource site and explore single cell applications and discover products that best match your needs. Take advantage of our extensive knowledge hub to access informative resources including webinars, posters, videos and scientific publications. ...

Every cell is unique. QIAGENs solutions accelerate single cell analysis in diverse research areas, from oncology, immunology and microbiology to neuroscience, stem cell and developmental biology, allowing you to access the smallest dimensions of biological research. Decipher the genomic and transcriptomic differences between cells and uncover the heterogeneity in your sample for new biological insights. Enter the world of the single cell through this dedicated resource site and explore single cell applications and discover products that best match your needs. Take advantage of our extensive knowledge hub to access informative resources including webinars, posters, videos and scientific publications. ...

Norwich Single-Cell Symposium 2019 http://www.earlham.ac.uk/single-cell-symposium-2019 https://tess.elixir-europe.org/events/norwich-single-cell-symposium-2019 Now in its third year, the Symposium covers single-cell genomics technologies and their application in microbial, plant, animal and human health and disease. The symposium offers a forum for researchers to discuss the latest developments in single-cell genomics, and network with other researchers with the intention of catalysing future development and application of single-cell genomics across the UK. Topics to be covered include: Single cell genomics in plant and microbial research Single cell genomics in health, disease and development Single cell informatics Single cell technology development 2019-10-16 10:00:00 UTC 2019-10-17 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ Earlham Institute [email protected] 10x ...

We would like aim to construct a platform made of fundamental analytical technologies that streamlines data-based single cell phenotyping. This platform is anticipated to realize quantitative, multiplexed analyses of a variety of biomolecules including nucleic acids, proteins, saccharides, lipids etc and the complex interactions at the intracellular and intercellular levels. Obviously, it requires diverse interdisciplinary approaches in nanotechnology, engineering, chemistry, optics, materials science, chemical biology, information science, which should be mixed with the steady progress in traditional biotechnology, on the basis of the deep understanding of real needs in life science communities. Therefore this Research Area welcomes ambitious young individuals to form a multidisciplinary virtual-network institute and nurtures them with its diversity to help them found their own unique technologies ...

The objective of this project is to study population genetics and genetic structure of phytoplankton based on single-cell genomics. Specifically, the focus will be on genomic variation in Gonyostomum semen (raphidophyceae), a harmful invasive microalga.. Populations of Gonyostomum have expanded invasively across N. Europe, but populations in N. America are less invasive and display less disruptive phenotypes despite similar environments. A population genomic approach can be used to explore the detailed dispersal patterns, and to understand the genetic basis of the differentiation among populations. By using single-cell genome amplification, the effort and bias of algal culturing is circumvented.. This research project is part of SINGEK, a Marie Skłodowska-Curie Innovative Training Network devised to provide a unique and structured training programme to a new generation of scientists with the highest expertise in Single Cell Genomics, from the initial stages of cell sorting to genome sequencing ...

Attracting researchers and technology developers, this meeting will explore the key challenges in Single Molecule & Single Cell Analysis. Speaker Biography

Attracting researchers and technology developers, this meeting will explore the key challenges in Single Molecule & Single Cell Analysis.

VALLEY COTTAGE, N.Y. - Future Market Insights (FMI) presents its new, comprehensive study on the global Single Cell Analysis System market spanning forecast. Researches at FMI have no left no stone unturned in bestowing readers a comprehensive view of the market, by studying the drivers, trends, challenges, and rest...

Single cell analysis is becoming increasingly important as it is clear that ensemble measurements mask the diversity of the biology in cell populations. Single...

Single Cell Analysis Market, report categorizes the report by Product, Technique, Application, End User. It provides information about - Global Industry Insights, Trends, Outlook, and Opportunity Analysis, 2018-2026

/PRNewswire/ -- The global Single Cell analysis market is expected to reach USD 5.0 billion by 2024, according to a new report published by Grand View...

Beckman Coulter Life Sciences discusses how single cell analysis for immunotherapy can be used and what it allows researchers to identify.

We present single-cell clustering using bifurcation analysis (SCUBA), a novel computational method for extracting lineage relationships from single-cell gene expression data and modeling the dynamic changes associated with cell differentiation. SCUBA draws techniques from nonlinear dynamics and stochastic differential equation theories, providing a systematic framework for modeling complex processes involving multilineage specifications. By applying SCUBA to analyze two complementary, publicly available datasets we successfully reconstructed the cellular hierarchy during early development of mouse embryos, modeled the dynamic changes in gene expression patterns, and predicted the effects of perturbing key transcriptional regulators on inducing lineage biases. The results were robust with respect to experimental platform differences between RT-PCR and RNA sequencing. We selectively tested our predictions in Nanog mutants and found good agreement between SCUBA predictions and the experimental ...

UCLA scientists have developed a NanoVelcro Chip that can detect and isolate single cancer cells from patient blood samples for analysis.. Researchers at UCLA report that they have refined a method they previously developed for capturing and analyzing cancer cells that break away from patients tumors and circulate in the blood. With the improvements to their device, which uses a Velcro-like nanoscale technology, they can now detect and isolate single cancer cells from patient blood samples for analysis.. Circulating tumor cells, or CTCs, play a crucial role in cancer metastasis, spreading from tumors to other parts of the body, where they form new tumors. When these cells are isolated from the blood early on, they can provide doctors with critical information about the type of cancer a patient has, the characteristics of the individual cancer and the potential progression of the disease. Doctors can also tell from these cells how to tailor a personalized treatment to a specific patient.. In ...

Achlatis, M, Pernice, M, Green, K, Guagliardo, P, Kilburn, MR, Hoegh-Guldberg, O and Dove, S (2018). Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge. ISME Journal 12(5): 1308-1318 ...

The human endocrine pancreas consists of multiple cell types and plays a critical role in glucose homeostasis. Here, we apply mass cytometry technology to measure all major islet hormones, proliferative markers, and readouts of signaling pathways involved in proliferation at single-cell resolution. Using this innovative technology, we simultaneously examined baseline proliferation levels of all endocrine cell types from birth through adulthood, as well as in response to the mitogen harmine. High-dimensional analysis of our marker protein expression revealed three major clusters of beta cells within individuals. Proliferating beta cells are confined to two of the clusters.. ...

The human endocrine pancreas consists of multiple cell types and plays a critical role in glucose homeostasis. Here, we apply mass cytometry technology to measure all major islet hormones, proliferative markers, and readouts of signaling pathways involved in proliferation at single-cell resolution. …

Offizielle Homepage der Friedrich-Schiller-Universität Jena, PF 07737 Jena, URL: http://www.uni-jena.de, Telefon: (49) 03641-9300, Webangebot der Friedrich-Schiller-Universität Jena // PhD position in Single Cell Genomics (m/f/d)

Exciting opportunity in Boston, MA for Massachusetts Eye and Ear, Harvard Medical School as a Postdoctoral Fellow in human genetics of complex eye diseases and single cell genomics

Setty, M., Tadmor, M.D., Reich-Zeliger, S. et al.. Recent single-cell analysis technologies offer an unprecedented opportunity to elucidate developmental pathways. Here we present Wishbone, an algorithm for positioning single cells along bifurcating developmental trajectories with high resolution. Wishbone uses multi-dimensional single-cell data, such as mass cytometry or RNA-Seq data, as input and orders cells according to their developmental progression, and it pinpoints bifurcation points by labeling each cell as pre-bifurcation or as one of two post-bifurcation cell fates. Using 30-channel mass cytometry data, we show that Wishbone accurately recovers the known stages of T-cell development in the mouse thymus, including the bifurcation point. We also apply the algorithm to mouse myeloid differentiation and demonstrate its generalization to additional lineages. A comparison of Wishbone to diffusion maps, SCUBA and Monocle shows that it outperforms these methods both in the accuracy of ...

Methodology from Fullerton and Moyer (2016). See paper for references cited below.. Sample collection. Subsurface sediments were collected on IODP expedition 331 (Deep Hot Biosphere) from 1 September through 4 October 2010 (Fig. 1). Onboard contamination testing of sites C0015 (126°53=E, 27°47=N; hole B; section 1H-5; 5.6mbsf) and C0017 (126°55=E, 27°47=N; hole C; section 1H-7; 26.6 m bsf) found no indication of interior-core contamination using fluorescent microspheres (both holes C0015B and C0017C) and perfluorocarbon tracer (hole C0017C only). The sample from hole C0017C was also verified by PCR-generated phylotype comparisons based on 97% similarity to phylotypes obtained from drilling mud at a contamination level of 1% or less (26). Subsamples were aseptically collected from the interiors of whole-round cores and stored in cryovials with 27% (vol/vol) glycerol at -80°C.. Single-cell source. Core depths were chosen from sites C0015 and C0017, which were characterized as weakly oxidized ...

January 07, 2015 Nodality, Inc. announced today the launch of its PathPro™ product line. PathPro products leverage the unique capabilities of Nodalitys proprietary Single Cell Network Profiling (SCNP) technology, offering predefined multiparametric flow cytometry-based experimental panels. These panels allow us to study customer inhibitor activity and identify disease subgroups and differential responses in pathways or diseases. Read more… ...

ACD has partnered with Indica Labs to offer quantitative RNAscope image analysis. This advanced digital pathology image analysis solution brings objective and accurate quantification to RNA in situ hybridization, enabling a new generation of applications based on single-cell analysis. With HALO, gene expression can be measured quantitatively at single-cell resolution and interpreted by pathologists within the histopathological context.

Nature - by Jeffrey M. Perkel - Data from thousands of single cells can be tricky to analyse, but software advances are making it easier. Single-cell biology is a hot topic these days. And at the cutting edge of the field is single-cell RNA sequencing (scRNA-seq). Conventional bulk methods of RNA sequencing (RNA-seq) process hundreds of thousands of cells at a time and average out the differences. But no two cells are exactly alike, and scRNA-seq can reveal the subtle changes that make each one unique. It can even reveal entirely new cell types. For instance, after using scRNA-seq to probe some 2,400 immune-system cells, Aviv Regev of the Broad Institute in Cambridge, Massachusetts, and her colleagues came across some dendritic cells that had potent T-cell-stimulating activity (A.-C. Villani et al. Science 356, eaah4573; 2017). Regev says that a vaccine to stimulate these cells could potentially boost the immune system and protect against cancer. But such discoveries are hard-won. Its much more

TTP Labtech, a global leader in the design and development of automated instrumentation and consumables for life science applications, and the University of California San Diego (UC San Diego), have announced that their collaboration has resulted in a new workflow for single cell sequencing, which reduces the cost of sample preparation by 90%.. The workflow, which has been published in the Journal of Laboratory Automation, was developed through the combination of UC San Diegos expertise in genomics and the use of TTP Labtechs mosquito liquid handlers, which can pipette nanolitre to microlitre volumes with high accuracy and reproducibility, to miniaturise and automate the process.. Although single-cell genomics is advancing rapidly, researchers face challenges linked with reproducibility, sensitivity, scalability and cost, particularly when trying to miniaturize high-throughput applications. To maximize accuracy and precision, library prep protocols recommend volumes that are within the range ...

Methods to rapidly assess cell growth would be useful for many applications, including drug susceptibility testing, but current technologies have limited sensitivity or throughput. Here we present an approach to precisely and rapidly measure growth rates of many individual cells simultaneously. We flow cells in suspension through a microfluidic channel with 10-12 resonant mass sensors distributed along its length, weighing each cell repeatedly over the 4-20 min it spends in the channel. Because multiple cells traverse the channel at the same time, we obtain growth rates for ,60 cells/h with a resolution of 0.2 pg/h for mammalian cells and 0.02 pg/h for bacteria. We measure the growth of single lymphocytic cells, mouse and human T cells, primary human leukemia cells, yeast, Escherichia coli and Enterococcus faecalis. Our system reveals subpopulations of cells with divergent growth kinetics and enables assessment of cellular responses to antibiotics and antimicrobial peptides within ...

Ellen has been a member of the research group of Susanne Mandrup since 2018, where she has been involved with work on transcriptional regulation in adipocytes during the development of obesity. Ellen, who has conducted her masters project as part of ATLAS, has been employed as a PhD student in ATLAS from September 2020 and has received a PhD scholarship from the Danish Diabetes Academy. The overarching aim of her PhD project is to understand adipose tissue plasticity and crosstalk between adipocytes and macrophages at single-cell resolution during regression of obesity. Her work includes the use of mouse- and human model systems, and application of RNA-sequencing at bulk-, cell-type specific-, and single-cell resolution.. ...

Since all cells are not alike, it is increasingly important to recognize the difference between cells for deeper insight into their behavior for tailored treatments in personalized medicine.

A team led by investigators at Cedars-Sinai Medical Center and the University of California, Los Angeles has developed a new approach for analyzing circulating tumor cells obtained from prostate cancer patients using chip- and sequencing-based applications.

Gene expression in multiple individual cells from a tissue or culture sample varies according to cell-cycle, genetic, epigenetic and stochastic differences between the cells. However, single-cell differences have been largely neglected in the analysis of the functional consequences of genetic variation. Here we measure the expression of 92 genes affected by Wnt signaling in 1,440 single cells from 15 individuals to associate single-nucleotide polymorphisms (SNPs) with gene-expression phenotypes, while accounting for stochastic and cell-cycle differences between cells. We provide evidence that many heritable variations in gene function--such as burst size, burst frequency, cell cycle-specific expression and expression correlation/noise between cells--are masked when expression is averaged over many cells. Our results demonstrate how single-cell analyses provide insights into the mechanistic and network effects of genetic variability, with improved statistical power to model these effects on gene

Because swine have a close resemblance to humans in terms of anatomy and physiology, the results of this study have several important implications for the clinical translation of iPSC therapy. First, we have shown that piPSCs can be successfully differentiated into a therapeutic cell population that mimics their endogenous counterparts, paving the way for the development of additional therapeutic subtypes. Second, we have demonstrated that the therapeutic effectiveness of piPSC-ECs in repairing the damaged myocardium is mediated by the release of proangiogenic and antiapoptotic modulating factors, using a novel microfluidic single-cell analysis. Third, we have also shown that the release of paracrine factors is highest among the subpopulation of piPSC-ECS expressing the endothelial specific markers CD34 and CD144, suggesting that transplantation of a subpopulation of these cells may lead to greater functional recovery. Finally, we have provided further validation of in vivo noninvasive ...

Johnson and Johnson will partner with Massachusetts General Hospital to develop and market a blood test that could find a single cancer cell circulating in a persons blood, the company said Monday.

TY - CHAP. T1 - Automated cell-by-cell tissue imaging and single-cell analysis for targeted morphologies by laser ablation electrospray ionization mass spectrometry. AU - Li, Hang. AU - Smith, Brian K.. AU - Shrestha, Bindesh. AU - Márk, L.. AU - Vertes, Akos. PY - 2014/10/31. Y1 - 2014/10/31. N2 - Mass spectrometry imaging (MSI) is an emerging technology for the mapping of molecular distributions in tissues. In most of the existing studies, imaging is performed by sampling on a predefined rectangular grid that does not reflect the natural cellular pattern of the tissue. Delivering laser pulses by a sharpened optical fiber in laser ablation electrospray ionization (LAESI) mass spectrometry (MS) has enabled the direct analysis of single cells and subcellular compartments. Cell-by-cell imaging had been demonstrated using LAESI-MS, where individual cells were manually selected to serve as natural pixels for tissue imaging. Here we describe a protocol for a novel cell-by-cell LAESI imaging approach ...

TY - JOUR. T1 - Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics. AU - Matsuda, Naoki. AU - Hironaka, Ken ichi. AU - Fujii, Masashi. AU - Wada, Takumi. AU - Kunida, Katsuyuki. AU - Inoue, Haruki. AU - Eto, Miki. AU - Hoshino, Daisuke. AU - Furuichi, Yasuro. AU - Manabe, Yasuko. AU - Fujii, Nobuharu L.. AU - Noji, Hiroyuki. AU - Imamura, Hiromi. AU - Kuroda, Shinya. N1 - Funding Information: We thank laboratory members for critical reading of the manuscript and for technical assistance with the analysis. The computations for this work were performed in part on the NIG supercomputer system at ROIS National Institute of Genetics. This work was supported by the Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics, CREST, of the Japan Science and Technology Agency (JST). S. K. was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Number ...

Supplementary MaterialsAdditional file 1: Additional figures. al. [5] are available under GEO accession number GSE56879. The scRRBS-seq data from HCCs, HepG2 cells and mESCs from Hou et al. [8] are available under GEO accession number GSE65364. Abstract Recent technological advances have enabled DNA methylation to be assayed at single-cell resolution. However, current protocols are limited by incomplete CpG coverage and hence methods to predict missing methylation says are critical to enable genome-wide analyses. We report DeepCpG, a computational approach based on deep neural networks to predict methylation expresses in one cells. We assess DeepCpG on single-cell methylation data from five cell types produced using substitute sequencing protocols. DeepCpG produces even more accurate predictions than prior strategies substantially. Additionally, we present the fact that Avasimibe cost model parameters could be interpreted, offering insights into how sequence composition impacts methylation ...

Background: Today, cells are commonly analyzed in ensembles, i.e. thousands of cells per sample, yielding results on the average response of the cells. However, cellular heterogeneity implies the importance of studying how individual cells respond, one by one, in order to learn more about drug targeting and cellular behavior. Scope of review: This review discusses general aspects on miniaturization of biological assays and in particular summarizes single-cell assays in microwell formats. A range of microwell-based chips are discussed with regard to their well characteristics, cell handling, choice of material etc. along with available detection systems for single-cell studies. History and trends in microsystem technology, various commonly used materials for device fabrication, and conventional methods for single-cell analysis are also discussed, before a closing section with a detailed example from our research in the field. Major conclusions:A range of miniaturized and microwell devices have ...

TY - JOUR. T1 - Single-cell analysis of Drosophila larval neuromuscular synapses. AU - Hoang, Bao. AU - Chiba, Akira. N1 - Funding Information: We thank the current members of Chiba lab for comments on the manuscript. This work was supported by grants from NIH/ NINDS and NSF (A.C.). Copyright: Copyright 2017 Elsevier B.V., All rights reserved.. PY - 2001/1/1. Y1 - 2001/1/1. N2 - The neuromuscular system of Drosophila has been widely used in studies on synaptic development. In the embryo, the cellular components of this model system are well established, with uniquely identified motoneurons displaying specific connectivity with distinct muscles. Such knowledge is essential to analyzing axon guidance and synaptic matching mechanisms with single-cell resolution. In contrast, to date the cellular identities of the larval neuromuscular synapses are hardly established. It is not known whether synaptic connections seen in the embryo persist, nor is it known how individual motor endings may ...

This webinar describes a groundbreaking new technique published recently in Analytical Chemistry for measuring single cancer cells. The study, conducted by Dr. David Walt and his research group at Tufts University, demonstrates that the ultrasensitive Simoa technology makes it possible to quantify phenotypic responses of individual prostate cancer cells.

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the oceans interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.. Read whole article in Science. ...

During mammalian early embryogenesis, expression and epigenetic heterogeneity emerge before the first cell fate determination, but the programs causing such determinate heterogeneity are largely unexplored. Here, we present MethylTransition, a novel DNA methylation state transition model, for characterizing methylation changes during one or a few cell cycles at single-cell resolution. MethylTransition involves the creation of a transition matrix comprising three parameters that represent the probabilities of DNA methylation-modifying activities in order to link the methylation states before and after a cell cycle. We apply MethylTransition to single-cell DNA methylome data from human pre-implantation embryogenesis and elucidate that the DNA methylation heterogeneity that emerges at promoters during this process is largely an intrinsic output of a program with unique probabilities of DNA methylation-modifying activities. Moreover, we experimentally validate the effect of the initial DNA methylation on

Characterizing various interacting cell types in the tumor microenvironment, and unraveling their underlying mechanisms can guide the development of improved and personalized cancer treatments. Azizis approach involves leveraging genomic profiling at single-cell resolution and developing machine learning and statistical method to analyze and integrate high-dimensional genomic data.. Azizi holds a BSc in Electrical Engineering from Sharif University of Technology (2008), and an MSc in Electrical Engineering (2010) and a PhD in Bioinformatics (2014) from Boston University. She was a postdoctoral fellow at Columbia University and Memorial Sloan Kettering Cancer Center (2014-2019). She joined the faculty of Columbia Biomedical Engineering and Irving Institute of Cancer Dynamics in 2020. She is also affiliated with the Department of Computer Science, Data Science Institute, and the Herbert Irving Comprehensive Cancer Center. ...

Lineage tracing at single-cell resolution reveals the presence of mesoteloblasts, the embryonic origin of mesodermal growth zone cells, and diverse cell cycling patterns of these lineages in the Polychaete annelid Platynereis.

Increased amounts of anti-neutrophil cytoplasm antibody (ANCA) directed against proteinase 3 (PR3) are a diagnostic and pathogenic hallmark of full-blown Wegeners granulomatosis (WG). Aggregates of B lymphocytes proximal to PR3+ cells as well as plasma cells have been described as substantial compo …

Recent advances in the field of stem cell biology and tissue engineering have made it possible to generate induced pluripotent stem (iPS) cells from somatic cells and to differentiate these iPS cells into many cell lineages and tissue types of the human body. We are using these technologies to study differentiation pathways and functional diversity of human cell types in controlled tissue culture environments. In parallel, we use single cell RNAseq to phenotype primary human tissues at multiple developmental stages in order to compare in vitro and in vivo patterns of development. Together, these approaches provide insight into the genetic mechanisms that build and maintain human organs. ...

Effect of pharmacologic kinase inhibition on normal hematopoietic signaling. Having established a baseline of healthy signaling responses to a panel of stimuli, we examined cell type-specific pharmacologic effects of some well-characterized kinase inhibitors. These included the Janus kinase (JAK) I inhibitor and MAPK kinase (MEK) inhibitor U0126. Predictably, when combined respectively with G-CSF and PMA/Ionomycin treatments of human BM (figs. S8 and S9) reliable and specific inhibition, respectively, of STAT3 and ERK1/2 phosphorylation are observed, which is consistent with previously reported observations that used conventional single-cell analysis platforms (44). Although interesting results were obtained with these inhibitors, we expanded to focus on dasatinib, a clinically relevant small-molecule kinase inhibitor. Dasatinib was originally introduced as a second-line BCR-ABL kinase inhibitor for imatinib-resistant chronic myelogenous leukemia (CML) (45). Unlike imatinib, dasatinib is ...

Single-cell transcriptome sequencing (scRNA-Seq), which combines high-throughput single-cell extraction and sequencing capabilities, enables the transcriptomes of large numbers of individual cells to be assayed efficiently.

The congruency of genomic and ITS phylogenies in Prochlorococcus at both coarse (4, 19) and fine resolution (Fig. 2) suggests that ITS-ribotype clusters coincide, in most cases, with distinct genomic backbones (15). This allowed us to estimate the number of coexisting backbone subpopulations in our samples through rarefaction analysis, revealing at least hundreds of coexisting subpopulations with distinct backbones (Fig. 4B) in each sample. These backbone subpopulations are estimated to have diverged at least a few million years ago (15), suggesting ancient, stable niche partitioning. That they have different alleles of genes associated with environmental interactions, carry a distinct set of flexible genes, and differ in relative abundance profiles as the environment changes suggests strongly that they are ecologically distinct.. Enormous population sizes and immense physical mixing probably played a role in the evolution of diverse genomic backbones in Prochlorococcus. A simple fluid mechanics ...

Preimplantation genetic diagnosis (PGD) aims to help couples with heritable genetic disorders to avoid the birth of diseased offspring or the recurrence of loss of conception. Following in vitro...

Symbiotic relationships between phytoplankton and N-2-fixing microorganisms play a crucial role in marine ecosystems. The abundant and widespread unicellular cyanobacteria group A (UCYN-A) has recently been found to live symbiotically with a haptophyte. Here, we investigated the effect of nitrogen (N), phosphorus (P), iron (Fe) and Saharan dust additions on nitrogen (N-2) fixation and primary production by the UCYN-A-haptophyte association in the subtropical eastern North Atlantic Ocean using nifH expression analysis and stable isotope incubations combined with single-cell measurements. N-2 fixation by UCYN-A was stimulated by the addition of Fe and Saharan dust, although this was not reflected in the nifH expression. CO2 fixation by the haptophyte was stimulated by the addition of ammonium nitrate as well as Fe and Saharan dust. Intriguingly, the single-cell analysis using nanometer scale secondary ion mass spectrometry indicates that the increased CO2 fixation by the haptophyte in treatments ...

TY - JOUR. T1 - Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity. AU - MacArthur, Ben D. AU - Sevilla, Ana. AU - Lenz, Michael. AU - Müller, Franz-Josef. AU - Schuldt, Berhard M. AU - Schuppert, Andreas A. AU - Ridden, Sonya J. AU - Stumpf, Patrick S. AU - Fidalgo, Miguel. AU - Maayan, Avi. AU - Wang, Jianlong. AU - Lemischka, Ihor R. PY - 2012/11. Y1 - 2012/11. N2 - A number of key regulators of mouse embryonic stem (ES) cell identity, including the transcription factor Nanog, show strong expression fluctuations at the single-cell level. The molecular basis for these fluctuations is unknown. Here we used a genetic complementation strategy to investigate expression changes during transient periods of Nanog downregulation. Employing an integrated approach that includes high-throughput single-cell transcriptional profiling and mathematical modelling, we found that early molecular changes subsequent to Nanog loss are stochastic and reversible. However, analysis ...

AbCellera today announced that the U.S. Patent and Trademark Office has granted patents on the use of microfluidics for high-throughput single-cell assays, with application in antibody discovery and clone selection, that extend protection of AbCelleras market-leading technology and adds to its expanding global intellectual property portfolio.

Glioblastoma is the most aggressive form of brain tumors showing resistance to treatment with various chemotherapeutic agents. The most effective way to eradicate glioblastoma requires the concurrent inhibition of multiple signaling pathways and target molecules involved in the progression of glioblastoma. Recently, we obtained a series of 1,2,3,4-tetrahydroisoquinoline alkaloids with potent anti-cancer activities, including ecteinascidin-770 (ET-770; the compound 1a) and renieramycin M (RM; the compound 2a) from Thai marine invertebrates, together with a 2-N-4

In the decade between 2004 and 2014 the rapid evolution of next generation sequencing (NGS) platforms reduced the cost of sequencing a gigabase of nucleic acid from $1000 to $10. The resultant availability of sequence data has caused a revolution in field of food microbiology. Outbreak investigation is an important activity in food microbiology and successfully delineating an outbreak relies primarily on a high-resolution comparison of the genetic relatedness of clinical, food, and environmental samples. Whole genome sequencing (WGS) provides the highest-resolution examination of the phylogenetic relatedness of isolates, and genomic data that is generated in the process can also be mined for the presence of virulence factors, antibiotic resistance genes, or other genetic markers of interest. Therefore, WGS is rapidly displacing other molecular typing methods for foodborne outbreak analysis and surveillance. Other sequencing techniques such as shot-gun metagenomics, single-cell sequencing, and 16S rRNA

Bioinformatics positions (Post-Doc) available at the Laboratory of Molecular Medicine and Genomics, University of Salerno. The Laboratory of Molecular Medicine and Genomics (http://www.labmedmolge.unisa.it/) is one of the largest and more experienced genomics research centers in Italy, with long-standing experience in generation and analysis of genomes, epigenomes and transcriptomes in human, plants, animals and bacteria. Its main research activities focus on genetics, epigenetics, oncogenomics and metagenomics and other fields of applications of NGS and microarrays technologies to Medicine, using standard as well as novel technologies, in particular single-cell sequencing and related.. The Laboratory is also home-base of Genomix4Life Srl (http://www.genomix4life.com/en/), a Company devoted to translational research in genomics and service provider of NGS, microarrays and related bioinformatics, that carries out most of its research in collaboration with personnel of the Laboratory.. We seek ...

Researchers have developed new single-cell sequencing methods that could be used to map the cell origins of various brain disorders, including Alzheimers, Parkinsons, schizophrenia and bipolar disorder.. By analyzing individual nuclei of cells from adult human brains, researchers at the University of California San Diego, Harvard Medical School and Sanford Burnham Prebys Medical Discovery Institute have identified 35 different subtypes of neurons and glial cells and discovered which of these subtypes are most susceptible to common risk factors for different brain diseases.. There are multiple theories regarding the roots of various brain diseases. Our findings enable us to narrow down and rank which types of cells in the brain carry the most genetic risk for developing these diseases, which can help drug developers pick better targets in the future, said Kun Zhang, a professor of bioengineering at the UC San Diego Jacobs School of Engineering and co-senior author of the study. Zhang is also ...

Patients suffering from Coronavirus disease 2019 (COVID-19) can develop neurological sequelae, such as headache, neuroinflammatory or cerebrovascular disease. These conditions - here termed Neuro-COVID - are more frequent in patients with severe COVID-19. To understand the etiology of these neurological sequelae, we utilized single-cell sequencing and examined the immune cell profiles from the cerebrospinal fluid (CSF) of Neuro-COVID patients compared to patients with non-inflammatory and autoimmune neurological diseases or with viral encephalitis. The CSF of Neuro-COVID patients exhibited an expansion of dedifferentiated monocytes and of exhausted CD4+ T cells. Neuro-COVID CSF leukocytes featured an enriched interferon signature; however, this was less pronounced than in viral encephalitis. Repertoire analysis revealed broad clonal T cell expansion and curtailed interferon response in severe compared to mild Neuro-COVID patients. Collectively, our findings document the CSF immune compartment in ...

I know something that you dont know will be the Science Slam of a LifeTime.. Researchers from the Max Delbrück Center for Molecular Medicine (MDC) will surprise the public with interesting and relevant facts about what we are made of. The scientists will explain what they are doing today to know more and how do they use this knowledge for the benefit of us all.. Each presentation will showcase LifeTime core technologies: single-cell sequencing, artificial intelligence and organoids. Science Slam of a Lifetime is a game show for those thirsty for knowledge.. At the end of the evening, the guests will decide: Who has told them something really new - and how useful is this knowledge?. November 2, 7:30 p.m. - 10 p.m., Umspannwerk Ost, Palisadenstraße 48, Berlin.. Free entry. English. Registration required ...

We have performed an in-depth single-cell phenotypic characterization of high-grade serous ovarian cancer (HGSOC) by multiparametric mass cytometry (CyTOF).

The UBC device - about the size of a nine-volt battery - allows scientists to simultaneously analyze 300 cells individually by routing fluid carrying cells through microscopic tubes and valves. Once isolated into their separate chambers, the cells RNA can be extracted and replicated for further analysis.. By enabling such single-cell analysis, the device could accelerate genetic research and hasten the use of far more detailed tests for diagnosing cancer.. Single-cell analysis is emerging as the gold standard of genetic research because tissue samples, even those taken from a single tumour, contain a mixture of normal cells and various types of cancer cells - the most important of which may be present in only very small numbers and impossible to distinguish.. So standard genetic tests, which require large numbers of cells, capture only an average composite picture of thousands or millions of different cells - obscuring their true nature and the interactions between them.. Its like trying ...

If you’re curious what innovations are coming out of the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative,...

Author summary In this study, we developed a workflow to detect and classify immune infiltrates in giga-pixel microscopy images. It allowed us to measure the degree of organization in lymphocyte clusters with graph-based features and finally to distinguish between tertiary lymphoid organs and other infiltrates. As a clinically relevant use case, we applied it to three different types of tissues and diseases. Our method addresses the need for observer-independent, large-scale evaluation of immune cell patterns and is a prerequisite to capture spatial composition of immune cells that can be used to parameterize mathematical models in systems immunology.

Advances in single cell genomics and transcriptomics have shown that at tissue level there is complex cellular heterogeneity. To understand the effect of this inter-cell heterogeneity on metabolism, it is essential to develop a single cell lipid profiling approach that allows the measurement of lipids in large numbers of single cells from a population. This will provide a functional readout of cell activity and membrane structure. Using liquid extraction surface analysis coupled with high-resolution mass spectrometry we have developed a high-throughput method for untargeted single cell lipid profiling. This technological advance highlighted the importance of cellular heterogeneity in the functional metabolism of individual human dopamine neurons, suggesting that A53T alpha-synuclein (SNCA) mutant neurons have impaired membrane function. These results demonstrate that this single cell lipid profiling platform can provide robust data that will expand the frontiers in biomedical research.. ...

Non-invasive single cell analyses are increasingly required for the medicaldiagnostics of test substances or the development of drugs and therapies on the single celllevel. For the non-invasive characterisation of cells, impedance spectroscopy whichprovides the frequency dependent electrical properties has been used. Recently,microfludic systems have been investigated to manipulate the single cells and tocharacterise the electrical properties of embedded cells. In this article, the impedance ofpartially embedded single cells dependent on the cellular behaviour was investigated byusing the microcapillary. An analytical equation was derived to relate the impedance ofembedded cells with respect to the morphological and physiological change ofextracellular interface. The capillary system with impedance measurement showed afeasibility to monitor the impedance change of embedded single cells caused bymorphological and physiological change of cell during the addition of DMSO. By fittingthe derived equation to

Profiling cells along the gut-brain axis at the single cell level will provide unique information for each cell type, a three-dimensional map of how cell types work together to form tissues, and insights into how changes in the map underlie health and disease of the GI system and its crosstalk with the brain. Disocver the latest research on single cell analysis of the gut-brain axis here. ...

Profiling cells along the gut-brain axis at the single cell level will provide unique information for each cell type, a three-dimensional map of how cell types work together to form tissues, and insights into how changes in the map underlie health and disease of the GI system and its crosstalk with the brain. Disocver the latest research on single cell analysis of the gut-brain axis here. ...

Snijder, B., R. Sacher, P. Ramo, P. Liberali, K. Mench, N. Wolfrum, L. Burleigh, C.C. Scott, M.H. Verheije, J. Mercer, S. Moese, T. Heger, K. Theusner, A. Jurgeit, D. Lamparter, G. Balistreri, M. Schelhaas, C.A. De Haan, V. Marjomaki, T. Hyypia, P.J. Rottier, B. Sodeik, M. Marsh, J. Gruenberg, A. Amara, U. Greber, A. Helenius, and L. Pelkmans. 2012. Single-cell analysis of population context advances RNAi screening at multiple levels. Mol Syst Biol. 8:579 ...

Single cell analysis is an important technology for biological and medical research. The precision of manipulating the location of the single cell (relative to the assay sites or other neighboring cells) is a necessary factor. We have previously demonstrated cell manipulation and separation with optoelectronic tweezers (OET), the goal of this project is to integrate this powerful tool with the micrifluidic devices to provide a complete solution for single cell electroporation ...

I am currently leading three research projects based on my expertise in micro- and nanofabrication combined with my experience in integrated sensors and microfluidics. The aim is to develop new methods for high-throughput screening needed in e.g. single cell analysis and drug screening. I am also interested in investigating the possibilities of nanotechnology and nanofabrication within the life sciences for the development of artificial models of human biological barriers. These in vitro models can be used for fundamental biological research as well as screening platforms in industry ...

UTHealth Flow Cytometry Service Center provides training, instrumentation and data analysis software to support your single cell analysis and sorting needs. We aim to use our technical and scientific expertise to help you achieve your research goals.. We currently have three flow cytometers and one cell sorter available to our customers in two separate locations. One analyzer and one cell sorter are located in our main facility at the Brown Foundation Institute for Molecular Medicine (IMM). This location provides full services, including assisted instrument usage. Our two other analyzers are located at the McGovern Medical School and are primarily reserved for unassisted operation by established users who have received instrument specific training. Both locations have additional workstations for post-acquisition data analysis.. ...

We have developed a quantitative assay to monitor the oxidative burst (H2O2 production) of polymorphonuclear leukocytes (PMNL) using single cell analysis by flow cytometry, and have examined whether PMNL respond to membrane stimulation with an all-or-none oxidative burst. During incubation with normal neutrophils, dichlorofluorescin diacetate diffused into the cells, was hydrolyzed to 2,7-dichlorofluorescin (DCFH) and was thereby trapped within the cells. The intracellular DCFH, a nonfluorescent fluorescein analogue, was oxidized to highly fluorescent 2,7-dichlorofluorescein (DCF) by PMNL stimulated by phorbol myristate acetate (PMA). That the oxidative product was DCF was shown by excitation/emission spectra and by mass spectrometry of the product from PMA-stimulated PMNL. Normal resting and PMA-stimulated PMNL oxidized 6.9 +/- 0.7 and 160 +/- 13 attomoles DCF per cell, respectively, in 15 min. Absence of calcium and magnesium ions and/or addition of 2 mM EDTA did not inhibit DCF formation ...

The Flow Cytometry Core aims to provide instrumentation and expertise in quantitative, high-speed, and multi-parameter fluorescence analysis (up to 7 fluorochromes) as well as single cell analysis and cell sorting services. The technology available will allow the researcher to quantify up to 7 markers for each cell and simultaneously sort multiple sub-populations of interest, which can then be cultured or analysed, with an array of molecular and cellular biology tools ...

We develop novel single cell analysis systems for scientists searching for rare and valuable biological variants across research, therapeutic, bioproduction and diagnostic applications. Our flexible technology, innovative products and range of services help you to boost throughput and sensitivity, while reducing costs and saving time ...

Tissue engineering is the combinational usage of cells, engineering, materials methods, suitable biochemical and physicochemical factors in order to improve or replace the infected biological tissues. The field includes the development of materials, devices, techniques to detect and differentiate disease states ,the treatment response, aid tissue healing, precisely deliver treatments to tissues or cells, signal early changes in health status, and provide implantable bio artificial replacement organs for recover or establish of healthy tissue .Techniques developed here identify and detect biomarkers of disease sub-types, progression, and treatment response, from tissue imaging, gene testing and gene analysis, that aid the more rapid development of new treatments and guide their clinical applications in treating the disorder. It includes the usage of computational modelling, bioinformatics and quantitative pharmacology to integrate data from diverse experimental and clinical sources to discover ...

Purpose: Adoptive T-cell therapy using autologous tumor-infiltrating lymphocytes (TIL) has shown an overall clinical response rate 40-50% in metastatic melanoma patients. BTLA (B-and-T lymphocyte attenuator) expression on transferred CD8+ TIL was associated with better clinical outcome. The suppressive function of the ITIM and ITSM motifs of BTLA is well described. Here, we sought to determine the functional characteristics of the CD8+BTLA+TIL subset and define the contribution of the Grb2 motif of BTLA in T cell co-stimulation. ,br /,,br /,Experimental Design: We determined the functional role and downstream signal of BTLA in both human CD8+ TIL and mouse CD8+ T cells. Functional assays were used including single cell analysis, Reverse Phase Protein Array (RPPA), antigen-specific vaccination models with adoptively transferred TCR-transgenic T cells as well as Patient-Derived Xenograft (PDX) model using Immunodeficient NOD-scid IL2Rgammanull (NSG) tumor-bearing mice treated with autologous ...

Single cell genomics is essential to chart the complex tumor ecosystem. While single cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumor tissues, single nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each strategy requires modifications to fit the unique characteristics of different tissue and tumor types, posing a barrier to adoption. Here, we developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We tested eight tumor types of varying tissue and sample characteristics (resection, biopsy, ascites, and orthotopic patient-derived xenograft): lung cancer, metastatic breast cancer, ovarian cancer, melanoma, neuroblastoma, pediatric sarcoma, glioblastoma, pediatric high-grade glioma, and chronic lymphocytic leukemia. Analyzing 212,498 cells and nuclei from 39 clinical samples, we evaluated protocols by cell quality, recovery rate, and cellular composition. We ...

A better understanding of the cell-fate transitions that occur in complex cellular ecosystems in normal development and disease could inform cell engineering efforts and lead to improved therapies. However, a major challenge is to simultaneously identify new cell states, and their transitions, to elucidate the gene expression dynamics governing cell-type diversification. Here, we present CellRouter, a multifaceted single-cell analysis platform that identifies complex cell-state transition trajectories by using flow networks to explore the subpopulation structure of multi-dimensional, single-cell omics data. We demonstrate its versatility by applying CellRouter to single-cell RNA sequencing data sets to reconstruct cell-state transition trajectories during hematopoietic stem and progenitor cell (HSPC) differentiation to the erythroid, myeloid and lymphoid lineages, as well as during re-specification of cell identity by cellular reprogramming of monocytes and B-cells to HSPCs. CellRouter opens previously

Flow cytometry is a widespread single-cell measurement technology with a multitude of clinical and research applications. Interpretation of flow cytometry data is hard; the instrumentation is delicate and can not render absolute measurements, hence samples can only be interpreted in relation to each other while at the same time comparisons are confounded by inter-sample variation. Despite this, most automated flow cytometry data analysis methods either treat samples individually or ignore the variation by for example pooling the data. A key requirement for models that include multiple samples is the ability to visualize and assess inferred variation, since what could be technical variation in one setting would be different phenotypes in another. We introduce BayesFlow, a pipeline for latent modeling of flow cytometry cell populations built upon a Bayesian hierarchical model. The model systematizes variation in location as well as shape. Expert knowledge can be incorporated through informative priors and

A key focus for the Oxford Consortium for Single-Cell Biology is to apply newly developed single-cell techniques to functional genomics. As part of this, the consortium is hosting Dave Ruff to help advance gene editing approaches at the single-cell level. Dave is a thought leader in the development of single-cell methods and will be presenting both the latest technologies and where he thinks the breakthroughs in single-cell systems biology over the next few years will be. Before joining Fluidigm in early 2013, Dave spent 17 years innovating qPCR and next-generation sequencing (NGS) technologies at Applied Biosystems/Life Technologies. He has been a lead investigator in the development of qPCR assays and chemistry, multiplex preamplification, protein quantification, NGS library preparation, sample-to-answer workflows, single-cell analysis, and nucleic acid sample-preparation processes. Prior to Applied Biosystems, Dave served as a research scientist at several early-stage biotechnology companies ...

Development and the associated cellular differentiation are some of the most fundamental processes in biology. Since the early conception of the Waddington landscape, with cells portrayed as rolling down a landscape, understanding these processes has been at the forefront of biology. Progress in tissue regeneration, organoid culture, and cellular reprogramming relies on our ability to unfold cellular decision making and its dynamics. In this thesis, we ask to what extent development follows such landscape. Secondly, we address whether cellular branching points are discrete events. Given the recent surge in single-cell genomics data, we can now address these fundamental questions. To this end, we analyzed two large-scale single-cell RNAseq time course datasets from vertebrate embryogenesis in zebrafish. From the Waddington analogy, we expect the cell-to-cell correlation to increase across development as cells specialize. Our analysis does not show a linear trend, but rather, that cell-to-cell ...

Fig. 2A shows the predicted identity of each cluster according to the above analysis. Representative top DE genes and GO pathways are indicated in Fig. 2D and SI Appendix, Fig. S2B, as well as Datasets S1 and S2. For identification purposes, we selected those whose expression is most specific to any given cluster vs. the rest. We detected two major groups of cells: Productal (clusters 1 to 4 in Fig. 2 D, Lower) and ducto-acinar (clusters 5 to 6 in Fig. 2 D, Upper). The distinction between ducto-acinar and productal is based on the DE of numerous acinar genes in clusters 5 to 6 (Fig. 2E and SI Appendix, Fig. S2A). Cluster 1 is represented by osteopontin/secreted phosphoprotein 1 (SPP1). This gene was previously identified as a marker of undifferentiated pancreatic progenitors in mice (14), and also by scRNA-seq in the developing mouse pancreas as a marker of proliferative ducts (15). Cluster 1 also has the highest PDX1 and inhibition of differentiation (ID)-1, -2, and -4 expression in the ...

Integration of single-cell resolution optogenetics and patch-clamp electrophysiology provides researchers with a detailed method to investigate neural circuit function. This Mightex application note details a microscopic setup for integrated single-cell resolution and patch-clamp electrophysiology.

Your sequencer. Our solutions. Powerful discovery. Whole Genome Sequencing Whole Exome Sequencing De novo Assembly Single Cell Genomics Single Cell V(D)J V

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