ArticleApplications in plant sciences2018
Comparing RNA-Seq and microarray gene expression data in two zones of the
Article in Applications in plant sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Hidden players in plant response to sulfur deficit and beyond: insights into the function of the proteins Sulfur Deficiency Induced and Response to Low Sulfur.Journal of experimental botany · 2026Review
- Plant Growth-Promoting Rhizobacteria and Bacterial Biocontrol Agents in Tomato Disease Management: Mechanisms, Applications, and Omics Perspectives.Global challenges (Hoboken, NJ) · 2025Review
- Accelerating crop improvement via integration of transcriptome-based network biology and genome editing.Planta · 2025Review
- Combined transcriptomic and proteomic analysis reveals the response mechanisms of alfalfa to freezing stress.Frontiers in plant science · 2025Article
- Systematic expression analysis of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 protein (CAP) superfamily inPlant direct · 2024Article
- Legume-rhizobia symbiosis: Translatome analysis.Genetics and molecular biology · 2024Article
- Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome.NPJ microgravity · 2023Article
- Test ofFrontiers in plant science · 2020Article
- Integrated analysis highlights multiple long non‑coding RNAs and their potential roles in the progression of human esophageal squamous cell carcinoma.Oncology reports · 2019Article
- Article
- Comparing RNA-Seq and microarray gene expression data in two zones of theApplications in plant sciences · 2018Article
Corrections and comments
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Authors and funding
3 authors.
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Abstract
premise of the studyThe root apex is an important region involved in environmental sensing, but comprises a very small part of the root. Obtaining root apex transcriptomes is therefore challenging when the samples are limited. The feasibility of using tiny root sections for transcriptome analysis was examined, comparing RNA sequencing (RNA-Seq) to microarrays in characterizing genes that are relevant to spaceflight.
methods
resultsBoth microarrays and RNA-Seq proved applicable to the small samples. A total of 4180 genes were differentially expressed (with fold changes of 2 or greater) between Zone 1 and Zone 2. In addition, 771 unique genes and 19 novel transcriptionally active regions were identified by RNA-Seq that were not detected in microarrays. However, microarrays detected spaceflight-relevant genes that were missed in RNA-Seq. DISCUSSION: Single root tip subsections can be used for transcriptome analysis using either RNA-Seq or microarrays. Both RNA-Seq and microarrays provided novel information. These data suggest that techniques for dealing with small, rare samples from spaceflight can be further enhanced, and that RNA-Seq may miss some spaceflight-relevant changes in gene expression.
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Registered trials
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