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
Citations
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Dysregulation of brain and choroid plexus cell types in severe COVID-19.
Andrew C. Yang,Fabian Kern,Patricia Moran Losada,Maayan R. Agam,Christina A. Maat,Georges Pierre Schmartz,Tobias Fehlmann,Julian A. Stein,Nicholas Schaum,Davis P. Lee,Kruti Calcuttawala,Ryan T. Vest,Daniela Berdnik,Nannan Lu,Oliver Hahn,David Gate,M. Windy McNerney,Divya Channappa,Inma Cobos,Nicole Ludwig,Walter J. Schulz-Schaeffer,Andreas Keller,Andreas Keller,Tony Wyss-Coray +23 more
TL;DR: In this article, single-nucleus transcriptomes of frontal cortex and choroid plexus samples from patients with COVID-19 reveal pathological cell states that are similar to those associated with human neurodegenerative diseases and chronic brain disorders.
Journal ArticleDOI
Sex Differences in Nucleus Accumbens Transcriptome Profiles Associated with Susceptibility versus Resilience to Subchronic Variable Stress
Georgia E. Hodes,Madeline L. Pfau,Immanuel Purushothaman,H. Francisca Ahn,Sam A. Golden,Daniel J. Christoffel,Jane Magida,Anna Brancato,Aki Takahashi,Meghan E. Flanigan,Caroline Menard,Hossein Aleyasin,Ja Wook Koo,Zachary S. Lorsch,Jian Feng,Mitra Heshmati,Minghui Wang,Gustavo Turecki,Rachel L. Neve,Bin Zhang,Li Shen,Eric J. Nestler,Scott J. Russo +22 more
TL;DR: It is reported that exposure to subchronic variable stress (SCVS) induces depression-associated behaviors in female mice, whereas males are resilient as they do not develop these behavioral abnormalities, and transcriptional analysis of nucleus accumbens revealed markedly different patterns of stress regulation of gene expression between the sexes.
Journal ArticleDOI
RNA-Seq workflow: gene-level exploratory analysis and differential expression
TL;DR: This work walks through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages to perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples.
Journal ArticleDOI
AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection
Thomas Vierbuchen,Emi Ling,Christopher J. Cowley,Cameron H. Couch,Xiaofeng Wang,David A. Harmin,Charles W. M. Roberts,Michael E. Greenberg +7 more
TL;DR: It is demonstrated how environmental signals acting via FOS/JUN and BAF coordinate with cell-type-specific TFs to select enhancer repertoires that enable differentiation during development.
Journal ArticleDOI
Transcription factor IRF4 Promotes CD8 + T cell exhaustion and limits the development of memory-like T cells during chronic infection
Kevin Man,Sarah S. Gabriel,Yang Liao,Yang Liao,Renee Gloury,Renee Gloury,Simon Preston,Simon Preston,Darren C. Henstridge,Marc Pellegrini,Marc Pellegrini,Dietmar Zehn,Friederike Berberich-Siebelt,Mark A. Febbraio,Wei Shi,Wei Shi,Axel Kallies,Axel Kallies +17 more
TL;DR: A transcriptional module consisting of the TCR‐induced transcription factors IRF4, BATF, and NFATc1 that drives T cell exhaustion and impairs memory T cell development is identified.
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