... , C. , Jha , S. , Batut , P. , Chaisson , M. and Gingeras , T. R. ( 2013 ). STAR: ultrafast universal RNA-seq aligner . Bioinformatics 29 , 15 - 21 . 10.1093/bioinformatics/bts635 Elenkov , I. J. , Webster , E. L. , Torpy , D. J. and Chrousos , G. P...

... patterns in the RNA-seq and proteomics data, the package FactoMineR ( Lê et al., 2008 ) in R was used to perform principal components analysis (PCA) on the normalized expression values of all samples for (1) RNA-seq and (2) proteomics data. The plotellipses function was used to draw confidence ellipses...

.... A. , Amit , I. , Adiconis , X. , Fan , L. , Raychowdhury , R. , Zeng , Q. et al. ( 2011 ). Full-length transcriptome assembly from RNA-Seq data without a reference genome . Nat. Biotechnol. 29 , 644 - 652 . 10.1038/nbt.1883 Gu , Z. , Eils , R. and Schlesner...

.... Transcriptomics Metabolomics Genomics RNA-seq Hypothesis testing A goal of comparative physiology is to understand the diverse mechanisms that allow animals to function and survive in their environments. Comparative physiologists (1) inquire vertically across levels of biological organization, (2...

... this article are available from the Dryad Digital Repository ( Delclos et al. 2020 ): dryad.76hdr7ssj . Raw sequencing data used for RNA-Seq analysis are deposited in NCBI's SRA (BioProject ID: PRJNA604205). All analyses of data in this study were conducted following pipelines described by the cited...

.../physiolgenomics.00016.2017 Roberts , A. , Trapnell , C. , Donaghey , J. , Rinn , J. L. and Pachter , L. ( 2011 ). Improving RNA-Seq expression estimates by correcting for fragment bias . Genome Biol.   12 , R22 . 10.1186/gb-2011-12-3-r22 Robinson , J. T...

... . Bioinformatics   21 , 2789 - 2790 . 10.1093/bioinformatics/bti394 Das , S. , Shyamal , S. and Durica , D. S. ( 2016 ). Analysis of annotation and differential expression methods used in RNA-seq studies in crustacean systems . Integr. Comp. Biol.   56 , 1067 - 1079 . 10.1093/icb/icw117...

.../ Summary: Honey bees caged for experimental purposes show significant alteration of their gene regulation and oxidative stress compared with their sister-mates operating under natural hive conditions. Honey bee RNA-seq Cage stress Imidacloprid Gene regulation Oxidative stress The honey...

... zebrafish retina reveals novel circadian transcripts. Zebrafish Retina Transcriptomics RNA-seq Circadian rhythms Circadian rhythms are physiological and behavioural changes that recur in about 24 h that allow the organism to adapt to fluctuations in the external environment driven...

..., such as RNA sequencing (RNA-seq). However, little attention has been given to how ecologically relevant field conditions may affect gene expression during diapause development because previous studies have focused on laboratory-reared and -maintained insects. To determine whether gene expression differs...

... Transcriptomics RNA-seq Biomineralization Shell formation (need 6-10) Thecosome pteropods, a group of marine planktonic shelled gastropods, contribute substantially to food webs and both carbon and carbonate flux in many pelagic ecosystems ( Berner and Honjo, 1981 ; Fabry and Deuser, 1991 ; Noji et...

... of transcriptomics to identify genes that underlie environmental adaptation is explored in the context of recent systems-level experiments that provide new insights into the relationship between gene expression and fitness. Environment Microarray Physiology RNA-seq Stress Temperature Transcriptomics...

... at a concentration of no less than 20 ng µl −1 on dry ice overnight to University Georgia. RNA-seq libraries from both constant and fluctuating temperature treatments at both early and late time points in 2010 were prepared using Illumina TruSeq mRNA standard protocol at the University of Georgia Genomics...

... that interchromosomal rearrangements played a role in the evolution of hypo-osmoregulation in Arctic charr. Read alignment to the reference transcriptome was conducted with RNA-Seq by expectation maximization (RSEM) ( Li and Dewey, 2011 ). RSEM performs accurate transcript quantification when a reference genome...

..., we use RNA-Seq to contrast gene expression during diapause with quiescence to identify transcriptional changes specific to the diapause response. We identify global trends in gene expression that show gradual convergence of diapause gene expression upon gene expression during quiescence. Functionally...