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single cell rna-seq

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https://www.readbyqxmd.com/read/28542535/a-trichostatin-a-expression-signature-identified-by-tempo-seq-targeted-whole-transcriptome-profiling
#1
Joanne M Yeakley, Peter J Shepard, Diana E Goyena, Harper C VanSteenhouse, Joel D McComb, Bruce E Seligmann
The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0...
2017: PloS One
https://www.readbyqxmd.com/read/28542205/rots-an-r-package-for-reproducibility-optimized-statistical-testing
#2
Tomi Suomi, Fatemeh Seyednasrollah, Maria K Jaakkola, Thomas Faux, Laura L Elo
Differential expression analysis is one of the most common types of analyses performed on various biological data (e.g. RNA-seq or mass spectrometry proteomics). It is the process that detects features, such as genes or proteins, showing statistically significant differences between the sample groups under comparison. A major challenge in the analysis is the choice of an appropriate test statistic, as different statistics have been shown to perform well in different datasets. To this end, the reproducibility-optimized test statistic (ROTS) adjusts a modified t-statistic according to the inherent properties of the data and provides a ranking of the features based on their statistical evidence for differential expression between two groups...
May 25, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28541377/asap-a-web-based-platform-for-the-analysis-and-interactive-visualization-of-single-cell-rna-seq-data
#3
Vincent Gardeux, Fabrice P A David, Adrian Shajkofci, Petra C Schwalie, Bart Deplancke
Motivation: Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research groups in the world, yet these groups often lack the expertise to handle complex scRNA-seq data sets. Results: We developed a fully integrated, web-based platform aimed at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28539161/single-cell-rna-seq-unveils-tumor-microenvironment
#4
Hae-Ock Lee, Woong-Yang Park
Single cell transcriptome analysis became an essential tool to define cell types or sub-populations within a heterogeneous bulk population. Tumor-associated microenvironment is a complex ecosystem with numerous cell types, supporting the tumor growth, angiogenesis, immune evasion, and metastasis. With the success of checkpoint inhibitors targeting the immune cell compartment, tumor microenvironment is an emerging anti-cancer target and its understanding becomes an imminent issue in the cancer biology.
May 25, 2017: BMB Reports
https://www.readbyqxmd.com/read/28535748/dtwscore-differential-expression-and-cell-clustering-analysis-for-time-series-single-cell-rna-seq-data
#5
Zhuo Wang, Shuilin Jin, Guiyou Liu, Xiurui Zhang, Nan Wang, Deliang Wu, Yang Hu, Chiping Zhang, Qinghua Jiang, Li Xu, Yadong Wang
BACKGROUND: The development of single-cell RNA sequencing has enabled profound discoveries in biology, ranging from the dissection of the composition of complex tissues to the identification of novel cell types and dynamics in some specialized cellular environments. However, the large-scale generation of single-cell RNA-seq (scRNA-seq) data collected at multiple time points remains a challenge to effective measurement gene expression patterns in transcriptome analysis. RESULTS: We present an algorithm based on the Dynamic Time Warping score (DTWscore) combined with time-series data, that enables the detection of gene expression changes across scRNA-seq samples and recovery of potential cell types from complex mixtures of multiple cell types...
May 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28534222/identification-of-innate-lymphoid-cells-in-single-cell-rna-seq-data
#6
Madeleine Suffiotti, Santiago J Carmona, Camilla Jandus, David Gfeller
Innate lymphoid cells (ILCs) consist of natural killer (NK) cells and non-cytotoxic ILCs that are broadly classified into ILC1, ILC2, and ILC3 subtypes. These cells recently emerged as important early effectors of innate immunity for their roles in tissue homeostasis and inflammation. Over the last few years, ILCs have been extensively studied in mouse and human at the functional and molecular level, including gene expression profiling. However, sorting ILCs with flow cytometry for gene expression analysis is a delicate and time-consuming process...
May 22, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28529717/gene-length-and-detection-bias-in-single-cell-rna-sequencing-protocols
#7
Belinda Phipson, Luke Zappia, Alicia Oshlack
Background: Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thousands of single cells. This technology has led to the discovery of novel cell types and revealed insights into the development of complex tissues. However, many technical challenges need to be overcome during data generation. Due to minute amounts of starting material, samples undergo extensive amplification, increasing technical variability. A solution for mitigating amplification biases is to include unique molecular identifiers (UMIs), which tag individual molecules...
2017: F1000Research
https://www.readbyqxmd.com/read/28528817/tracing-and-characterizing-the-development-of-transplanted-female-germline-stem-cells-in%C3%A2-vivo
#8
Changqing Wu, Bo Xu, Xiaoyong Li, Wenzhi Ma, Ping Zhang, Xuejin Chen, Ji Wu
It has long been believed that most female mammalian species lose the ability to generate oocytes in postnatal ovaries. Recent evidence has demonstrated the isolation and culture of female germline stem cells (FGSCs) from adult mice and humans. However, the process and mechanisms of FGSC differentiation in vivo following transplantation have not yet been studied. Here, we isolated and characterized FGSCs from a single EGFP-transgenic mouse, and traced the development and behavior of transplanted FGSCs (F-TFs) in vivo...
May 6, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28526029/cell-fixation-and-preservation-for-droplet-based-single-cell-transcriptomics
#9
Jonathan Alles, Nikos Karaiskos, Samantha D Praktiknjo, Stefanie Grosswendt, Philipp Wahle, Pierre-Louis Ruffault, Salah Ayoub, Luisa Schreyer, Anastasiya Boltengagen, Carmen Birchmeier, Robert Zinzen, Christine Kocks, Nikolaus Rajewsky
BACKGROUND: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not altered by stress or ageing. Other challenges are rare cells that need to be collected over several days or samples prepared at different times or locations. METHODS: Here, we used chemical fixation to address these problems...
May 19, 2017: BMC Biology
https://www.readbyqxmd.com/read/28524227/computational-approaches-for-interpreting-scrna-seq-data
#10
REVIEW
R Rostom, V Svensson, S A Teichmann, G Kar
The recent developments in high throughput single-cell RNA sequencing technology (scRNA-seq) have enabled the generation of vast amounts of transcriptomic data at cellular resolution. With these advances come new modes of data analysis, building on high-dimensional data mining techniques. Here, we consider biological questions for which scRNA-seq data is used, both at a cell and gene level, and describe tools available for these types of analyses. This is an exciting and rapidly evolving field, where clustering, pseudotime inference, branching inference and gene-level analyses are particularly informative areas of computational analysis...
May 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28521784/functional-regression-method-for-whole-genome-eqtl-epistasis-analysis-with-sequencing-data
#11
Kelin Xu, Li Jin, Momiao Xiong
BACKGROUND: Epistasis plays an essential rule in understanding the regulation mechanisms and is an essential component of the genetic architecture of the gene expressions. However, interaction analysis of gene expressions remains fundamentally unexplored due to great computational challenges and data availability. Due to variation in splicing, transcription start sites, polyadenylation sites, post-transcriptional RNA editing across the entire gene, and transcription rates of the cells, RNA-seq measurements generate large expression variability and collectively create the observed position level read count curves...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28514690/genomic-characterization-of-murine-monocytes-reveals-c-ebp%C3%AE-transcription-factor-dependence-of-ly6c-cells
#12
Alexander Mildner, Jörg Schönheit, Amir Giladi, Eyal David, David Lara-Astiaso, Erika Lorenzo-Vivas, Franziska Paul, Louise Chappell-Maor, Josef Priller, Achim Leutz, Ido Amit, Steffen Jung
Monocytes are circulating, short-lived mononuclear phagocytes, which in mice and man comprise two main subpopulations. Murine Ly6C(+) monocytes display developmental plasticity and are recruited to complement tissue-resident macrophages and dendritic cells on demand. Murine vascular Ly6C(-) monocytes patrol the endothelium, act as scavengers, and support vessel wall repair. Here we characterized population and single cell transcriptomes, as well as enhancer and promoter landscapes of the murine monocyte compartment...
May 16, 2017: Immunity
https://www.readbyqxmd.com/read/28503665/probabilistic-modeling-of-bifurcations-in-single-cell-gene-expression-data-using-a-bayesian-mixture-of-factor-analyzers
#13
Kieran R Campbell, Christopher Yau
Modeling bifurcations in single-cell transcriptomics data has become an increasingly popular field of research. Several methods have been proposed to infer bifurcation structure from such data, but all rely on heuristic non-probabilistic inference. Here we propose the first generative, fully probabilistic model for such inference based on a Bayesian hierarchical mixture of factor analyzers. Our model exhibits competitive performance on large datasets despite implementing full Markov-Chain Monte Carlo sampling, and its unique hierarchical prior structure enables automatic determination of genes driving the bifurcation process...
March 15, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28501348/single-cell-rna-sequencing-unraveling-the-brain-one-cell-at-a-time
#14
REVIEW
Dimitry Ofengeim, Nikolaos Giagtzoglou, Dann Huh, Chengyu Zou, Junying Yuan
Single-cell RNA sequencing (scRNA-seq) is an exciting new technology allowing the analysis of transcriptomes from individual cells, and is ideally suited to address the inherent complexity and dynamics of the central nervous system. scRNA-seq has already been applied to the study of molecular taxonomy of the brain. These works have paved the way to expanding our understanding of the nervous system and provide insights into cellular susceptibilities and molecular mechanisms in neurological and neurodegenerative diseases...
May 10, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28499021/protein-only-rnase-p-function-in-escherichia-coli-viability-processing-defects-and-differences-between-prorp-isoenzymes
#15
Markus Gößringer, Marcus Lechner, Nadia Brillante, Christoph Weber, Walter Rossmanith, Roland K Hartmann
The RNase P family comprises structurally diverse endoribonucleases ranging from complex ribonucleoproteins to single polypeptides. We show that the organellar (AtPRORP1) and the two nuclear (AtPRORP2,3) single-polypeptide RNase P isoenzymes from Arabidopsis thaliana confer viability to Escherichia coli cells with a lethal knockdown of its endogenous RNA-based RNase P. RNA-Seq revealed that AtPRORP1, compared with bacterial RNase P or AtPRORP3, cleaves several precursor tRNAs (pre-tRNAs) aberrantly in E. coli...
May 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28495919/alternative-tsss-are-co-regulated-in-single-cells-in-the-mouse-brain
#16
Kasper Karlsson, Peter Lönnerberg, Sten Linnarsson
Alternative transcription start sites (TSSs) have been extensively studied genome-wide for many cell types and have been shown to be important during development and to regulate transcript abundance between cell types. Likewise, single-cell gene expression has been extensively studied for many cell types. However, how single cells use TSSs has not yet been examined. In particular, it is unknown whether alternative TSSs are independently expressed, or whether they are co-activated or even mutually exclusive in single cells...
May 11, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28488141/elevated-t-cell-activation-score-is-associated-with-improved-survival-of-breast-cancer
#17
Lingeng Lu, Yalai Bai, Zuoheng Wang
PURPOSE: Immune checkpoints cytotoxic T lymphocyte antigen 4 (CTLA4) and programmed cell death 1 receptor (PD-1) negatively regulate CD8(+) T cell functions, impeding the capacity of effector T cells to kill tumors. Here, we study the prognostic significance of CTLA4, PD-1 and T cell activation status in breast cancer. METHODS: Using a publicly accessed RNA-seq dataset including 1087 breast cancer patients, we performed Kaplan-Meier survival curves and multivariate Cox regression models to evaluate the associations of CTLA4, PD-1, and weighted T cell activation score with patients' overall survival...
May 9, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28479188/vitamin-a-retinoic-acid-signaling-regulates-hematopoietic-stem-cell-dormancy
#18
Nina Cabezas-Wallscheid, Florian Buettner, Pia Sommerkamp, Daniel Klimmeck, Luisa Ladel, Frederic B Thalheimer, Daniel Pastor-Flores, Leticia P Roma, Simon Renders, Petra Zeisberger, Adriana Przybylla, Katharina Schönberger, Roberta Scognamiglio, Sandro Altamura, Carolina M Florian, Malak Fawaz, Dominik Vonficht, Melania Tesio, Paul Collier, Dinko Pavlinic, Hartmut Geiger, Timm Schroeder, Vladimir Benes, Tobias P Dick, Michael A Rieger, Oliver Stegle, Andreas Trumpp
Dormant hematopoietic stem cells (dHSCs) are atop the hematopoietic hierarchy. The molecular identity of dHSCs and the mechanisms regulating their maintenance or exit from dormancy remain uncertain. Here, we use single-cell RNA sequencing (RNA-seq) analysis to show that the transition from dormancy toward cell-cycle entry is a continuous developmental path associated with upregulation of biosynthetic processes rather than a stepwise progression. In addition, low Myc levels and high expression of a retinoic acid program are characteristic for dHSCs...
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28474673/single-cell-rna-seq-enables-comprehensive-tumour-and-immune-cell-profiling-in-primary-breast-cancer
#19
Woosung Chung, Hye Hyeon Eum, Hae-Ock Lee, Kyung-Min Lee, Han-Byoel Lee, Kyu-Tae Kim, Han Suk Ryu, Sangmin Kim, Jeong Eon Lee, Yeon Hee Park, Zhengyan Kan, Wonshik Han, Woong-Yang Park
Single-cell transcriptome profiling of tumour tissue isolates allows the characterization of heterogeneous tumour cells along with neighbouring stromal and immune cells. Here we adopt this powerful approach to breast cancer and analyse 515 cells from 11 patients. Inferred copy number variations from the single-cell RNA-seq data separate carcinoma cells from non-cancer cells. At a single-cell resolution, carcinoma cells display common signatures within the tumour as well as intratumoral heterogeneity regarding breast cancer subtype and crucial cancer-related pathways...
May 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28474362/identification-of-physical-interactions-between-genomic-regions-by-enchip-seq
#20
Toshitsugu Fujita, Miyuki Yuno, Yutaka Suzuki, Sumio Sugano, Hodaka Fujii
Physical interactions between genomic regions play critical roles in the regulation of genome functions, including gene expression. Here, we show the feasibility of using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) in combination with next-generation sequencing (NGS) (enChIP-Seq) to detect such interactions. In enChIP-Seq, the target genomic region is captured by an engineered DNA-binding complex, such as a clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a catalytically inactive form of Cas9 and a single guide RNA...
May 5, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
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