Statistical Design and Analysis of RNA Sequencing Data

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A survey of best practices for RNA-seq data analysis

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rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

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How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

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RNA Sequencing and Analysis

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From RNA-seq reads to differential expression results

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Microarrays, deep sequencing and the true measure of the transcriptome

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RNA-seq differential expression studies: more sequence or more replication?

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Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

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Design and computational analysis of single-cell RNA-sequencing experiments

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Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

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Reducing Astrocyte Calcium Signaling In Vivo Alters Striatal Microcircuits and Causes Repetitive Behavior

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Transcriptomics in the RNA-seq era

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DrImpute: imputing dropout events in single cell RNA sequencing data

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The fate of duplicated genes in a polyploid plant genome

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RNA-seq: technical variability and sampling

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Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

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Injured adult neurons regress to an embryonic transcriptional growth state

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Design and validation issues in RNA-seq experiments

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The power and promise of RNA ‐seq in ecology and evolution

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Designing a transcriptome next‐generation sequencing project for a nonmodel plant species1

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Principles of transcriptome analysis and gene expression quantification: an RNA ‐seq tutorial

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Targeted enrichment strategies for next‐generation plant biology

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Comparative Transcriptomics of Convergent Evolution: Different Genes but Conserved Pathways Underlie Caste Phenotypes across Lineages of Eusocial Insects

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Classification and clustering of sequencing data using a Poisson model

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ISEV position paper: extracellular vesicle RNA analysis and bioinformatics

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Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes

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Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress

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RNAi screens in mice identify physiological regulators of oncogenic growth

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ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

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powsimR: power analysis for bulk and single cell RNA-seq experiments

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Whole-transcriptome RNAseq analysis from minute amount of total RNA

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De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

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Tomato plants increase their tolerance to low temperature in a chilling acclimation process entailing comprehensive transcriptional and metabolic adjustments

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Experimental design for single-cell RNA sequencing

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Behavioral and neurogenomic transcriptome changes in wild-derived zebrafish with fluoxetine treatment

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Astrocyte–neuron subproteomes and obsessive–compulsive disorder mechanisms

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Models for transcript quantification from RNA-SeqPreprint

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Context-Specific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable

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Extracellular vesicles and their nucleic acids for biomarker discovery

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On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

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Plastic and Evolved Responses to Global Change: What Can We Learn from Comparative Transcriptomics?: Table 1.

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The evolution of gene expression and the transcriptome–phenotype relationship

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quantro: a data-driven approach to guide the choice of an appropriate normalization method

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Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers

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Systems biology approaches to new vaccine development

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Shaping development through mechanical strain: the transcriptional basis of diet‐induced phenotypic plasticity in a cichlid fish

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Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size

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Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow

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Genomic toolboxes for conservation biologists

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Current RNA-seq methodology reporting limits reproducibility

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A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq

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Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel

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RNA‐seq Data: Challenges in and Recommendations for Experimental Design and Analysis

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A MYB Triad Controls Primary and Phenylpropanoid Metabolites for Pollen Coat Patterning

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RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection

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Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2by RNA-Seq

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Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models

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Variation in RNA-Seq Transcriptome Profiles of Peripheral Whole Blood from Healthy Individuals with and without Globin Depletion

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Transcriptomics analysis revealing candidate networks and genes for the body size sexual dimorphism of Chinese tongue sole (Cynoglossus semilaevis)

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Effects of library size variance, sparsity, and compositionality on the analysis of microbiome dataPreprint

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Impact of low dose oral exposure to bisphenol A (BPA) on the neonatal rat hypothalamic and hippocampal transcriptome: a clarity-BPA consortium study

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Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

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multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments

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Comparison of differential accessibility analysis strategies for ATAC-seq data

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Microbiome of Deep Dentinal Caries from Reversible Pulpitis to Irreversible Pulpitis

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RNA-Sequencing: A tool to explore new frontiers in animal genetics

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Phylogenetic Analysis of Gene Expression

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RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia

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Next-Generation Sequencing for MicroRNA Expression Profile

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Comparison of normalization approaches for gene expression studies completed with high-throughput sequencing

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Omics approaches for the assessment of biological responses to nanoparticles

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RNA-Seq Provides New Insights in the Transcriptome Responses Induced by the Carcinogen Benzo[a]pyrene

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Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm–Mosquito Interactions

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Dynamics of the chili pepper transcriptome during fruit development

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RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum

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Multi-study inference of regulatory networks for more accurate models of gene regulation

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Mycobacterial infection induces a specific human innate immune response

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Analysis of gene expression changes in peach leaves in response to P lum pox virus infection using RNA ‐ S eq

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RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis

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Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio)

Wong, R. Y., McLeod, M. M., & Godwin, J. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-905 · Cited by 70

RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism

Resnyk, C., Chen, C., Huang, H., Wu, C. H., Simon, J., Bihan-Duval, É. L., Duclos, M. J. M. J., & Cogburn, L. A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0139549 · Cited by 66

LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS

Yang, Y., Fear, J. M., Hu, J., Häecker, I., Zhou, L. J., Renne, R., Bloom, D. C., & McIntyre, L. M. (2014) · Computational and Structural Biotechnology Journal · doi:10.5936/csbj.201401002 · Cited by 63

So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute

Willette, D. A., Allendorf, F. W., Barber, P. H., Barshis, D. J., Carpenter, K. E., Crandall, E. D., Cresko, W. A., Fernández-Silva, I., Matz, M. V., Meyer, E., et al. (2014) · Bulletin of Marine Science · doi:10.5343/bms.2013.1008 · Cited by 64

Transcriptome changes specifically associated with apple (Malus domestica) root defense response during Pythium ultimum infection

Shin, S., Zheng, P., Fazio, G., Mazzola, M., Main, D., & Zhu, Y. (2016) · Physiological and Molecular Plant Pathology · doi:10.1016/j.pmpp.2016.03.003 · Cited by 63

Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development

Radhakrishnan, S., Literman, R., Neuwald, J. L., Severin, A. J., & Valenzuela, N. (2017) · PLoS ONE · doi:10.1371/journal.pone.0172044 · Cited by 66

miRNA expression profiles and molecular networks in resting and LPS-activated BV-2 microglia—Effect of cannabinoids

Juknat, A., Gao, F., Coppola, G., Vogel, Z., & Kozela, E. (2019) · PLoS ONE · doi:10.1371/journal.pone.0212039 · Cited by 67

Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods

Mäder, U., Nicolas, P., Richard, H., Bessières, P., & Aymerich, S. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.10.003 · Cited by 62

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

Fumagalli, D., Blanchet-Cohen, A., Brown, D. N., Desmedt, C., Gacquer, D., Michiels, S., Rothé, F., Majjaj, S., Salgado, R., Larsimont, D., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-1008 · Cited by 60

Transcriptomic Insight Into the Polygenic Mechanisms Underlying Psychiatric Disorders

Hernandez, L. M., Kim, M., Hoftman, G. D., Haney, J. R., de la Torre-Ubieta, L., Paşaniuc, B., & Gandal, M. J. (2020) · Biological Psychiatry · doi:10.1016/j.biopsych.2020.06.005 · Cited by 59

Meta‐analysis and meta‐regression of transcriptomic responses to water stress in Arabidopsis

Rest, J. S., Wilkins, O., Wei, Y., Purugganan, M. D., & Gurevitch, J. (2016) · The Plant Journal · doi:10.1111/tpj.13124 · Cited by 59

Glia Open Access Database ( GOAD ): A comprehensive gene expression encyclopedia of glia cells in health and disease

Holtman, I. R., Noback, M. A., Bijlsma, M., Duong, K. N., van der Geest, M. A., Ketelaars, P. T., Brouwer, N., Vainchtein, I. D., Eggen, B. J. L., & Boddeke, H. W. G. M. (2015) · Glia · doi:10.1002/glia.22810 · Cited by 57

A comparison of analog and Next-Generation transcriptomic tools for mammalian studies

Roy, N. C., Altermann, E., Park, Z. A., & McNabb, W. C. (2011) · Briefings in Functional Genomics · doi:10.1093/bfgp/elr005 · Cited by 58

Transcriptome Analysis in Domesticated Species: Challenges and Strategies

Hekman, J. P., Johnson, J. L., & Kukekova, A. V. (2015) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s29334 · Cited by 62

ISSUE HIGHLIGHTS

(2010) · Genetics · doi:10.1093/genetics/185.2.np · Cited by 1

Design of RNA Sequencing Experiments

Nettleton, D. S. (2014) · Springer eBooks · doi:10.1007/978-3-319-07212-8_5 · Cited by 6

Design and validation issues in RNA-seq experiments

Fang, Z., & Cui, X. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr004 · Cited by 243

Biological Perspectives of RNA-Sequencing Experimental Design

Pasmanik‐Chor, M. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1103-6_17 · Cited by 2

Modeling and Analysis of Next-Generation Sequencing Data

Lin, S., Scholtens, D. M., & Datta, S. (2022) · Chapman & Hall/CRC eBooks · doi:10.1201/9781315153728-5