voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Charity W. Law,Charity W. Law,Yunshun Chen,Yunshun Chen,Wei Shi,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TLDR
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments, and the voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline.Abstract:
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.read more
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Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks.
John M Bryan,Temesgen D. Fufa,Kapil Bharti,Brian P. Brooks,Robert B. Hufnagel,David M. McGaughey +5 more
TL;DR: This work collated all publicly available healthy human eye RNA-seq datasets as well as dozens of other tissues to probe the biological processes and pan expression relationships between the cornea, retina, retinal pigment epithelium (RPE)-choroid complex, and the rest of the human tissues with differential expression, clustering and gene ontology term enrichment tools.
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Comparative analysis of single-cell RNA-sequencing methods
Christoph Ziegenhain,Swati Parekh,Beate Vieth,Martha Smets,Heinrich Leonhardt,Ines Hellmann,Wolfgang Enard +6 more
TL;DR: Smart-seq2 is the most sensitive method as it detects the most genes per cell and across cells, however, it shows more amplification noise than CEL-seq, Drop-seq and SCRB-seq as it cannot use unique molecular identifiers (UMIs).
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C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
Kaido Lepik,Tarmo Annilo,Viktorija Kukuškina,Kai Kisand,Zoltán Kutalik,Pärt Peterson,Hedi Peterson +6 more
TL;DR: Computational analysis and cell culture stimulation assays revealed increased CRP levels to drive the expression of complement regulatory protein CD59, suggesting CRP to have a critical role in protecting blood cells from the adverse effects of the immune defence system.
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Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis.
Anna Shcherbina,Jacqueline Larouche,Paula Fraczek,Benjamin A. Yang,Lemuel A. Brown,James F. Markworth,Carolina H Chung,Mehwish Khaliq,Kanishka de Silva,Jeongmoon J. Choi,Mohammad Fallahi-Sichani,Mohammad Fallahi-Sichani,Sriram Chandrasekaran,Young C. Jang,Susan V. Brooks,Carlos A. Aguilar +15 more
TL;DR: An integrative genomics approach is used to profile MuSCs from young and aged animals before and after injury and reveals aging impacts multiple regulatory changes through significant differences in gene expression, metabolic flux, chromatin accessibility, and patterns of transcription factor (TF) binding activities.
Journal ArticleDOI
IL-7 receptor blockade blunts antigen-specific memory T cell responses and chronic inflammation in primates
Lyssia Belarif,Caroline Mary,Lola Jacquemont,Hoa Le Mai,Richard Danger,Jeremy Hervouet,David Minault,Virginie Thepenier,Véronique Nerrière-Daguin,Elisabeth Nguyen,Sabrina Pengam,Eric Largy,Arnaud Delobel,Bernard Martinet,Stéphanie Le Bas-Bernardet,Sophie Brouard,Jean-Paul Soulillou,Nicolas Degauque,Gilles Blancho,Bernard Vanhove,Nicolas Poirier +20 more
TL;DR: It is shown that a single dose of anti-IL-7 receptor monoclonal antibody that exhibits antagonist but not agonist properties can reduce the frequency of antigen-specific T cell to help repress chronic skin inflammation.
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