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single cell rna-seq

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https://www.readbyqxmd.com/read/28100584/umi-tools-modelling-sequencing-errors-in-unique-molecular-identifiers-to-improve-quantification-accuracy
#1
Tom Sean Smith, Andreas Heger, Ian Sudbery
Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR-amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalised. In particular, sequencing errors in the UMI sequence are often ignored, or else resolved in an ad-hoc manner. We show that errors in the UMI sequence are common and introduce network based methods to account for these errors when identifying PCR duplicates...
January 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28100273/erratum-to-quartz-seq-a-highly-reproducible-and-sensitive-single-cell-rna-sequencing-method-reveals-non-genetic-gene-expression-heterogeneity
#2
Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda
No abstract text is available yet for this article.
January 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28099430/pooled-crispr-screening-with-single-cell-transcriptome-readout
#3
Paul Datlinger, André F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler, Johanna Klughammer, Linda C Schuster, Amelie Kuchler, Donat Alpar, Christoph Bock
CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome profiling, but at much lower throughput. Here we combine pooled CRISPR screening with single-cell RNA sequencing into a broadly applicable workflow, directly linking guide RNA expression to transcriptome responses in thousands of individual cells...
January 18, 2017: Nature Methods
https://www.readbyqxmd.com/read/28098555/nematophagous-fungus-arthrobotrys-oligospora-mimics-olfactory-cues-of-sex-and-food-to-lure-its-nematode-prey
#4
Yen-Ping Hsueh, Matthew R Gronquist, Erich M Schwarz, Ravi David Nath, Ching-Han Lee, Shalha Gharib, Frank C Schroeder, Paul W Sternberg
To study the molecular basis for predator-prey coevolution, we investigated how Caenorhabditis elegans responds to the predatory fungus Arthrobotrys oligospora. C. elegans and other nematodes were attracted to volatile compounds produced by A. oligospora. Gas-chromatographic mass-spectral analyses of A. oligospora-derived volatile metabolites identified several odors mimicking food cues attractive to nematodes. One compound, methyl 3-methyl-2-butenoate (MMB) additionally triggered strong sex- and stage-specific attraction in several Caenorhabditis species...
January 18, 2017: ELife
https://www.readbyqxmd.com/read/28096075/hpprna-a-snakemake-based-handy-parameter-free-pipeline-for-rna-seq-analysis-of-numerous-samples
#5
Dapeng Wang
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for an easy-to-learn workflow to cope with the increased demands from a large number of laboratories across the world. We report a one-in-all solution called hppRNA, composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection, written by a series of individual Perl and R scripts, counting on well-established and preinstalled software, irrespective of single-end or paired-end, unstranded or stranded sequencing method...
January 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28094291/differential-effects-of-vitamins-a-and-d-on-the-transcriptional-landscape-of-human-monocytes-during-infection
#6
Tilman E Klassert, Julia Bräuer, Martin Hölzer, Magdalena Stock, Konstantin Riege, Cristina Zubiría-Barrera, Mario M Müller, Silke Rummler, Christine Skerka, Manja Marz, Hortense Slevogt
Vitamin A and vitamin D are essential nutrients with a wide range of pleiotropic effects in humans. Beyond their well-documented roles in cellular differentiation, embryogenesis, tissue maintenance and bone/calcium homeostasis, both vitamins have attracted considerable attention due to their association with-immunological traits. Nevertheless, our knowledge of their immunomodulatory potential during infection is restricted to single gene-centric studies, which do not reflect the complexity of immune processes...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28093458/single-cell-gene-expression-analysis-reveals-diversity-among-human-spermatogonia
#7
N Neuhaus, J Yoon, N Terwort, S Kliesch, J Seggewiss, A Huge, R Voss, S Schlatt, R V Grindberg, H R Schöler
STUDY QUESTION: Is the molecular profile of human spermatogonia homogeneous or heterogeneous when analysed at the single-cell level? SUMMARY ANSWER: Heterogeneous expression profiles may be a key characteristic of human spermatogonia, supporting the existence of a heterogeneous stem cell population. WHAT IS KNOWN ALREADY: Despite the fact that many studies have sought to identify specific markers for human spermatogonia, the molecular fingerprint of these cells remains hitherto unknown...
January 15, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28092691/effective-detection-of-variation-in-single-cell-transcriptomes-using-matq-seq
#8
Kuanwei Sheng, Wenjian Cao, Yichi Niu, Qing Deng, Chenghang Zong
The quantification of transcriptional variation in single cells, particularly within the same cell population, is currently limited by the low sensitivity and high technical noise of single-cell RNA-seq assays. We report multiple annealing and dC-tailing-based quantitative single-cell RNA-seq (MATQ-seq), a highly sensitive and quantitative method for single-cell sequencing of total RNA. By systematically determining technical noise, we show that MATQ-seq captures genuine biological variation between whole transcriptomes of single cells...
January 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/28088763/scater-pre-processing-quality-control-normalization-and-visualization-of-single-cell-rna-seq-data-in-r
#9
Davis J McCarthy, Kieran R Campbell, Aaron T L Lun, Quin F Wills
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. RESULTS: We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28061811/the-nature-and-nurture-of-cell-heterogeneity-accounting-for-macrophage-gene-environment-interactions-with-single-cell-rna-seq
#10
Quin F Wills, Esther Mellado-Gomez, Rory Nolan, Damien Warner, Eshita Sharma, John Broxholme, Benjamin Wright, Helen Lockstone, William James, Mark Lynch, Michael Gonzales, Jay West, Anne Leyrat, Sergi Padilla-Parra, Sarah Filippi, Chris Holmes, Michael D Moore, Rory Bowden
BACKGROUND: Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome's limitations in describing higher functional phenotypes and protein events. Perhaps the most important shortfall with transcriptomic 'snapshots' of cell populations is that they risk being descriptive, only cataloging heterogeneity at one point in time, and without microenvironmental context. Studying the genetic ('nature') and environmental ('nurture') modifiers of heterogeneity, and how cell population dynamics unfold over time in response to these modifiers is key when studying highly plastic cells such as macrophages...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28061332/in%C3%A2-vivo-cleavage-map-illuminates-the-central-role-of-rnase-e-in-coding-and-non-coding-rna-pathways
#11
Yanjie Chao, Lei Li, Dylan Girodat, Konrad U Förstner, Nelly Said, Colin Corcoran, Michał Śmiga, Kai Papenfort, Richard Reinhardt, Hans-Joachim Wieden, Ben F Luisi, Jörg Vogel
Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis...
January 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28060364/single-cell-transcriptomics-of-small-microbial-eukaryotes-limitations-and-potential
#12
Zhenfeng Liu, Sarah K Hu, Victoria Campbell, Avery O Tatters, Karla B Heidelberg, David A Caron
Single-cell transcriptomics is an emerging research tool that has huge untapped potential in the study of microbial eukaryotes. Its application has been tested in microbial eukaryotes 50 μm or larger, and it generated transcriptomes similar to those obtained from culture-based RNA-seq. However, microbial eukaryotes have a wide range of sizes and can be as small as 1 μm. Single-cell RNA-seq was tested in two smaller protists (8 and 15 μm). Transcript recovery rate was much lower and randomness in observed gene expression levels was much higher in single-cell transcriptomes than those derived from bulk cultures of cells...
January 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28056792/elucidation-of-the-molecular-responses-of-a-cucumber-segment-substitution-line-carrying-pm5-1-and-its-recurrent-parent-triggered-by-powdery-mildew-by-comparative-transcriptome-profiling
#13
Qiang Xu, Xuewen Xu, Yang Shi, Xiaohua Qi, Xuehao Chen
BACKGROUND: Powdery mildew (PM) is one of the most severe fungal diseases of cucurbits, but the molecular mechanisms underlying PM resistance in cucumber remain elusive. In this study, we developed a PM resistant segment substitution line SSL508-28 that carried a segment on chromosome five representing the Pm5.1 locus from PM resistant donor Jin5-508 using marker-assisted backcrossing of an elite PM susceptible cucumber inbred line D8. RESULTS: Whole-genome resequencing of SSL508-28, Jin5-508 and D8 was performed to identify the exact boundaries of the breakpoints for this introgression because of the low density of available single sequence repeat markers...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28049429/jacusa-site-specific-identification-of-rna-editing-events-from-replicate-sequencing-data
#14
Michael Piechotta, Emanuel Wyler, Uwe Ohler, Markus Landthaler, Christoph Dieterich
BACKGROUND: RNA editing is a co-transcriptional modification that increases the molecular diversity, alters secondary structure and protein coding sequences by changing the sequence of transcripts. The most common RNA editing modification is the single base substitution (A→I) that is catalyzed by the members of the Adenosine deaminases that act on RNA (ADAR) family. Typically, editing sites are identified as RNA-DNA-differences (RDDs) in a comparison of genome and transcriptome data from next-generation sequencing experiments...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28045572/rna-seq-unveils-new-attributes-of-the-heterogeneous-salmonella-host-cell-communication
#15
Francisco García-Del Portillo, M Graciela Pucciarelli
High-throughput RNA sequencing (RNA-Seq) has uncovered hundreds of small RNAs and complex modes of RNA regulation in every bacterium analyzed to date. This complexity agrees with the adaptability of most bacteria to varied environments including, in the case of pathogens, the new niches encountered in the host. Recent RNA-Seq studies have analyzed simultaneously gene expression in the intracellular pathogen Salmonella enterica and infected host cells at population and single-cell level. Distinct polarization states or interferon responses in the infected macrophage were linked to variable growth rates or activities of defined virulence regulators in intra-phagosomal bacteria...
January 3, 2017: RNA Biology
https://www.readbyqxmd.com/read/28045081/batch-effects-and-the-effective-design-of-single-cell-gene-expression-studies
#16
Po-Yuan Tung, John D Blischak, Chiaowen Joyce Hsiao, David A Knowles, Jonathan E Burnett, Jonathan K Pritchard, Yoav Gilad
Single-cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene expression levels at high resolution. However, the sources of experimental noise in scRNA-seq are not yet well understood. We investigated the technical variation associated with sample processing using the single-cell Fluidigm C1 platform. To do so, we processed three C1 replicates from three human induced pluripotent stem cell (iPSC) lines. We added unique molecular identifiers (UMIs) to all samples, to account for amplification bias...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28028040/whole-genome-expression-analysis-of-mammalian-wide-interspersed-repeat-elements-in-human-cell-lines
#17
Davide Carnevali, Anastasia Conti, Matteo Pellegrini, Giorgio Dieci
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution...
December 27, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28025200/falco-a-quick-and-flexible-single-cell-rna-seq-processing-framework-on-the-cloud
#18
Andrian Yang, Michael Troup, Peijie Lin, Joshua W K Ho
: : Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here we introduce Falco, a cloud-based framework to enable paralellization of existing RNA-seq processing pipelines using big data technologies of Apache Hadoop and Apache Spark for performing massively parallel analysis of large scale transcriptomic data...
December 24, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28018394/global-transcriptional-analysis-reveals-the-complex-relationship-between-tea-quality-leaf-senescence-and-the-responses-to-cold-drought-combined-stress-in-camellia-sinensis
#19
Chao Zheng, Yu Wang, Zhaotang Ding, Lei Zhao
In field conditions, especially in arid and semi-arid areas, tea plants are often simultaneously exposed to various abiotic stresses such as cold and drought, which have profound effects on leaf senescence process and tea quality. However, most studies of gene expression in stress responses focus on a single inciting agent, and the confounding effect of multiple stresses on crop quality and leaf senescence remain unearthed. Here, global transcriptome profiles of tea leaves under separately cold and drought stress were compared with their combination using RNA-Seq technology...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28011883/single-cell-transcriptomic-profiling-of-mouse-pancreatic-progenitors
#20
Diana E Stanescu, Reynold Yu, Kyoung Jae Won, Doris A Stoffers
The heterogeneity of the developing pancreatic epithelium and low abundance of endocrine progenitors limits the information derived from traditional expression studies. To identify genes that characterize early developmental tissues composed of multiple progenitor lineages, we applied single-cell RNA-Seq to embryonic day (e)13.5 mouse pancreata and performed integrative analysis with single cell data from mature pancreas. We identified subpopulations expressing macrophage or endothelial markers and new pancreatic progenitor markers...
December 23, 2016: Physiological Genomics
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