Analysis and visualization of RNA-Seq expression data using RStudio, Bioconductor, and Integrated Genome Browser.
Ann E. Loraine,Ivory C. Blakley,Sridharan Jagadeesan,Jeffrey F. Harper,Gad Miller,Nurit Firon +5 more
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TLDR
This protocol describes using R Markdown and RStudio, user-friendly tools for statistical analysis and reproducible research in bioinformatics, to analyze and document the analysis of an example RNA-Seq data set from tomato pollen undergoing chronic heat stress.Abstract:
Sequencing costs are falling, but the cost of data analysis remains high, often because unforeseen problems arise, such as insufficient depth of sequencing or batch effects Experimenting with data analysis methods during the planning phase of an experiment can reveal unanticipated problems and build valuable bioinformatics expertise in the organism or process being studied This protocol describes using R Markdown and RStudio, user-friendly tools for statistical analysis and reproducible research in bioinformatics, to analyze and document the analysis of an example RNA-Seq data set from tomato pollen undergoing chronic heat stress Also, we show how to use Integrated Genome Browser to visualize read coverage graphs for differentially expressed genes Applying the protocol described here and using the provided data sets represent a useful first step toward building RNA-Seq data analysis expertise in a research groupread more
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A decade of pollen transcriptomics.
Nicholas Rutley,David Twell +1 more
TL;DR: Historical evidence for male haploid gene expression is outlined and the wealth of pollen transcriptome data now available is reviewed to inspire new directions and the application of system-based research into the mechanisms that govern the development, function and evolution of angiosperm pollen.
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Human DNA-PK activates a STING-independent DNA sensing pathway
Katelyn Burleigh,Joanna H. Maltbaek,Stephanie Cambier,Richard Green,Michael Gale,Richard C. James,Richard C. James,Daniel B. Stetson +7 more
TL;DR: It is shown here that humans—but not laboratory mice—have a second, potent, STING-independent DNA sensing pathway (SIDSP) and human DNA-dependent protein kinase (DNA-PK) is identified as the sensor of this pathway and demonstrated that DNA-PK activity drives a robust and broad antiviral response.
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Interferon-λ modulates dendritic cells to facilitate T cell immunity during infection with influenza A virus.
TL;DR: It is demonstrated that IFN-λ is essential for effective adaptive cellular immunity in the lung and serves a critical role in bridging innate and adaptive immunity from lung mucosa to lymph nodes to program DCs to direct effective T cell immunity against IAV.
Journal ArticleDOI
Data Integration for Future Medicine (DIFUTURE).
TL;DR: The infrastructure envisioned by DIFUTURE will provide researchers with cross-site access to data and support physicians by innovative views on integrated data as well as by decision support components for personalized treatments, with a specific focus on data integration and sharing.
References
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TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
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The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Ugrappa Nagalakshmi,Zhong Wang,Karl Waern,C. Shou,Debasish Raha,Mark Gerstein,Michael Snyder +6 more
TL;DR: A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed.
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Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
Ryan Lister,Ronan C. O'Malley,Julian Tonti-Filippini,Brian D. Gregory,Charles C. Berry,A. Harvey Millar,Joseph R. Ecker +6 more
TL;DR: Deep sequencing of smRNAs revealed a direct relationship between the location of sm RNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylisation, and a tendency for smRN as to direct strand-specific DNA methylations in regions of RNA-DNA homology.