ArticleScientific reports2016
Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics.
Article in Scientific reports, 2016. 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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11 citing papers in PubMed.
- A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination.Nature plants · 2026Article
- Article
- Immunochemical Identification of the Main Cell Wall Polysaccharides of the Early Land PlantCells · 2023Article
- AtEXT3 is not essential for early embryogenesis or plant viability in Arabidopsis.The New phytologist · 2022Article
- Spatial transcriptomics: new dimension of understanding biological complexity.Biophysics reports · 2022Article
- RNA In Situ Hybridization of Paraffin Sections to Characterize the Multicellular Compartmentation of Plant Secondary Metabolisms.Methods in molecular biology (Clifton, N.J.) · 2022Article
- An integrative Study Showing the Adaptation to Sub-Optimal Growth Conditions of Natural Populations ofCells · 2020Article
- The Class III Peroxidase Encoding GeneInternational journal of molecular sciences · 2020Article
- Demystifying biotrophs: FISHing for mRNAs to decipher plant and algal pathogen-host interaction at the single cell level.Scientific reports · 2020Article
- TheFrontiers in plant science · 2017Article
- A Comparative Study of Sample Preparation for Staining and Immunodetection of Plant Cell Walls by Light Microscopy.Frontiers in plant science · 2017Article
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7 authors.
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Abstract
The rationale of this study is to compare and integrate two heterologous datasets intended to unravel the spatiotemporal specificities of gene expression in a rapidly growing and complex organ. We implemented medium-throughput RNA in situ hybridization (ISH) for 39 genes mainly corresponding to cell wall proteins for which we have particular interest, selected (i) on their sequence identity (24 class III peroxidase multigenic family members and 15 additional genes used as positive controls) and (ii) on their expression levels in a publicly available Arabidopsis thaliana seed tissue-specific transcriptomics study. The specificity of the hybridization signals was carefully studied, and ISH results obtained for the 39 selected genes were systematically compared with tissue-specific transcriptomics for 5 seed developmental stages. Integration of results illustrates the complementarity of both datasets. The tissue-specific transcriptomics provides high-throughput possibilities whereas ISH provides high spatial resolution. Moreover, depending on the tissues and the developmental stages considered, one or the other technique appears more sensitive than the other. For each tissue/developmental stage, we finally determined tissue-specific transcriptomic threshold values compatible with the spatiotemporally-specific detection limits of ISH for lists of hundreds to tens-of-thousands of genes.
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