ReviewFrontiers in plant science2023
Design, execution, and interpretation of plant RNA-seq analyses.
Review in Frontiers in plant science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed.
- Volatiles released by undamaged plants mediate the adaptive growth strategies in neighbors.Journal of experimental botany · 2026Article
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- ROS-Centered Transcriptomic Regulatory Networks Linking Salinity Stress, Antioxidant Defense and Processability Traits inCurrent issues in molecular biology · 2026Review
- Identification of circadian-regulated genes for enhancing acidic soil tolerance in rice through integrative transcriptomic and systems analysis.Scientific reports · 2026Article
- Integrated Metabolome and Transcriptome Analysis in Ammi majus L. Revealed Candidate Genes of Furanocoumarins Pathway.Biochemical genetics · 2026Article
- Stress-Induced Plant Specialized Metabolism: Signaling, Multi-Omics Integration, and Plant-Derived Antimicrobial Metabolites to Combat Antimicrobial Resistance.Plants (Basel, Switzerland) · 2026Review
- WGCNA reveals dose-dependent responses and molecular regulatory networks of strigolactone-mediated drought mitigation inFrontiers in plant science · 2026Article
- AI-integrated digital breeding for crop improvement.Frontiers in plant science · 2026Review
- Harnessing multi-omics and genome-editing technologies for climate-resilient agriculture: bridging AI-driven insights with sustainable crop improvement.Plant molecular biology · 2025Review
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Use of Field pathogenomics approach for Puccinia striiformis f. sp. tritici race identification and phylogenomic delineation in North India.World journal of microbiology & biotechnology · 2025Article
- Genetic and molecular insights into tiller development and approaches for crop yield improvement.Frontiers in plant science · 2025Review
- Next-generation data filtering in the genomics era.Nature reviews. Genetics · 2024Review
- Zinc finger knuckle genes are associated with tolerance to drought and dehydration in chickpea (Frontiers in plant science · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences. We discuss the importance of experimental design in RNA-seq, including considerations for sampling and replication, to avoid pitfalls and wasted resources. Approaches for processing RNA-seq data include quality control and counting features, and we describe common approaches and variations. Though differential gene expression analysis is the most common analysis of RNA-seq data, we review multiple methods for assessing gene expression, including detecting allele-specific gene expression and building co-expression networks. With the production of more RNA-seq data, strategies for integrating these data into genetic mapping pipelines is of increased interest. Finally, special considerations for RNA-seq analysis and interpretation in plants are needed, due to the high genome complexity common across plants. By incorporating informed decisions throughout an RNA-seq experiment, we can increase the knowledge gained.
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Registered trials
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