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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Neonatal and adult recent thymic emigrants produce IL-8 and express complement receptors CR1 and CR2.
Marcin L. Pekalski,Arcadio Rubio García,Ricardo C. Ferreira,Daniel B. Rainbow,Deborah J. Smyth,Meghavi Mashar,Jane Brady,Natalia Savinykh,Xaquin Castro Dopico,Sumiyya Mahmood,Simon Duley,Helen Stevens,Neil Walker,Antony J. Cutler,Frank Waldron-Lynch,David B. Dunger,Claire Shannon-Lowe,Alasdair Coles,Joanne L Jones,Chris Wallace,John A. Todd,Linda S. Wicker +21 more
TL;DR: It is defined that the naive T cells having divided the least since thymic emigration express complement receptors (CR1 and CR2) known to bind complement C3b- and C3d-decorated microbial products and produce IL-8, a major chemoattractant for neutrophils in bacterial defense.
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In Vivo Labeling by CD73 Marks Multipotent Stromal Cells and Highlights Endothelial Heterogeneity in the Bone Marrow Niche
Martin Breitbach,Kenichi Kimura,Kenichi Kimura,Tiago C. Luis,Christopher J. Fuegemann,Petter S. Woll,Petter S. Woll,Michael Hesse,Raffaella Facchini,Sarah Rieck,Katarzyna Jobin,Julia Reinhardt,Osamu Ohneda,Daniela Wenzel,Caroline Geisen,Christian Kurts,Wolfgang Kastenmüller,Michael Hölzel,Sten Eirik W. Jacobsen,Bernd K. Fleischmann +19 more
TL;DR: The CD73-EGFP mouse is a powerful tool for studying MSCs and sinusoidal endothelium and reveals an endothelial subtype that also displays a mesenchymal signature, highlighting endothelial cell heterogeneity in the marrow.
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Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion
Yasmine J. Liu,Georges E. Janssens,Rebecca L. McIntyre,Marte Molenaars,Rashmi Kamble,Arwen W. Gao,Aldo Jongejan,Michel van Weeghel,Alyson W. MacInnes,Riekelt H. Houtkooper +9 more
TL;DR: It is shown that supplementation of glycine significantly prolongs C. elegans lifespan, and early adulthood is important for its salutary effects, while RNA-sequencing reveals a similar transcriptional landscape in serine- and glycine-supplemented worms both demarked by widespread gene repression.
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BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome
TL;DR: These findings demonstrate that BRG1 establishes specialized chromatin environments that define multiple classes of GBSs and predicts that GR and other transcriptional activators function via multiple distinct chromatin-based mechanisms to modulate the transcriptional response.
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A molecular roadmap of the AGM region reveals BMPER as a novel regulator of HSC maturation.
Alison McGarvey,Stanislav Rybtsov,Celine Souilhol,Sara Tamagno,Ritva Rice,David Hills,Duncan Godwin,David P. Rice,Simon R. Tomlinson,Alexander Medvinsky +9 more
TL;DR: It is demonstrated that BMPER is associated with BMP signaling inhibition, but is transcriptionally induced by BMP4, suggesting that B MPER contributes to the precise control of BMP activity within the AGM region, enabling the maturation of HSCs within a BMP-negative environment.
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