Dataset

Rice (Oryza sativa) dataset from detailed molecular profiling uncovering dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice coleoptiles under anoxia and re-oxygenation

La Trobe University
Professor James Whelan (Principal investigator) Dr Mathew G. Lewsey (Managed by) Mr Andrew Robinson (Managed by)
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.4225/22/5934b50c9c524&rft.title=Rice (Oryza sativa) dataset from detailed molecular profiling uncovering dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice coleoptiles under anoxia and re-oxygenation&rft.identifier=10.4225/22/5934b50c9c524&rft.publisher=La Trobe University&rft.description=This dataset originates from research carried out in 2016, published in the paper Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. The RNA-seq data generated provides a detailed molecular profile of Oryza sativa enabling the identification of differentially expressed genes and uncovers the essential features for germination and early seedling growth under anoxic conditions.The data provide insights into the molecular responses to oxygen deprivation. An extensive time course was examined, from dry seeds to germinating embryos (24 h) and up to 4-day-old rice coleoptiles, as well as coleoptiles collected from seedlings grown for 3 days under anoxic conditions and transferred to air for one day.In rice, germination and seedling development can progress in both the presence and absence of oxygen. While the transcriptomic responses to anaerobic conditions, found using microarrays, have revealed common responses, even across kingdoms, these alone are not sufficient for altering tolerance to anaerobic conditions. An in-depth study was undertaken which resulted in data creation from several time points during germination and in the rice coleoptile using RNA-seq analyses.&rft.creator=Robinson, Andrew &rft.creator=Narsai, Reena &rft.creator=Lewsey, Mathew &rft.creator=Whelan, James &rft.date=2018&rft_rights=Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/&rft_subject=Plant Cell and Molecular Biology&rft_subject=Biological Sciences&rft_subject=Plant Biology&rft_subject=Plant Developmental and Reproductive Biology&rft_subject=Crop and Pasture Biochemistry and Physiology&rft_subject=Agricultural and Veterinary Sciences&rft_subject=Crop and Pasture Production&rft_subject=Crop and Pasture Improvement (Selection and Breeding)&rft_subject=Rice&rft_subject=Plant Production and Plant Primary Products&rft_subject=Summer Grains and Oilseeds&rft_subject=Oryza Sativa&rft_subject=Rna-Seq&rft_subject=Dna Methylation&rft_subject=Anoxia&rft_subject=Anaerobic&rft_subject=Low Oxygen&rft_place=Melbourne&rft.type=dataset&rft.language=English ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.4225/22/5934b50c9c524&rft.title=Rice (Oryza sativa) dataset from detailed molecular profiling uncovering dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice coleoptiles under anoxia and re-oxygenation&rft.identifier=10.4225/22/5934b50c9c524&rft.publisher=La Trobe University&rft.description=This dataset originates from research carried out in 2016, published in the paper Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. The RNA-seq data generated provides a detailed molecular profile of Oryza sativa enabling the identification of differentially expressed genes and uncovers the essential features for germination and early seedling growth under anoxic conditions.The data provide insights into the molecular responses to oxygen deprivation. An extensive time course was examined, from dry seeds to germinating embryos (24 h) and up to 4-day-old rice coleoptiles, as well as coleoptiles collected from seedlings grown for 3 days under anoxic conditions and transferred to air for one day.In rice, germination and seedling development can progress in both the presence and absence of oxygen. While the transcriptomic responses to anaerobic conditions, found using microarrays, have revealed common responses, even across kingdoms, these alone are not sufficient for altering tolerance to anaerobic conditions. An in-depth study was undertaken which resulted in data creation from several time points during germination and in the rice coleoptile using RNA-seq analyses.&rft.creator=Robinson, Andrew &rft.creator=Narsai, Reena &rft.creator=Lewsey, Mathew &rft.creator=Whelan, James &rft.date=2018&rft_rights=Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/&rft_subject=Plant Cell and Molecular Biology&rft_subject=Biological Sciences&rft_subject=Plant Biology&rft_subject=Plant Developmental and Reproductive Biology&rft_subject=Crop and Pasture Biochemistry and Physiology&rft_subject=Agricultural and Veterinary Sciences&rft_subject=Crop and Pasture Production&rft_subject=Crop and Pasture Improvement (Selection and Breeding)&rft_subject=Rice&rft_subject=Plant Production and Plant Primary Products&rft_subject=Summer Grains and Oilseeds&rft_subject=Oryza Sativa&rft_subject=Rna-Seq&rft_subject=Dna Methylation&rft_subject=Anoxia&rft_subject=Anaerobic&rft_subject=Low Oxygen&rft_place=Melbourne&rft.type=dataset&rft.language=English Access the data

Licence & Rights:

Open Licence view details
CC-BY

Creative Commons Attribution
https://creativecommons.org/licenses/by/4.0/

Contact Information

Street Address:
La Trobe Genomics Platform
Centre for AgriBioscience
5 Ring Road
La Trobe University
Bundoora, Vic 3086
Australia



Full description

This dataset originates from research carried out in 2016, published in the paper "Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation." The RNA-seq data generated provides a detailed molecular profile of Oryza sativa enabling the identification of differentially expressed genes and uncovers the essential features for germination and early seedling growth under anoxic conditions.

The data provide insights into the molecular responses to oxygen deprivation. An extensive time course was examined, from dry seeds to germinating embryos (24 h) and up to 4-day-old rice coleoptiles, as well as coleoptiles collected from seedlings grown for 3 days under anoxic conditions and transferred to air for one day.

In rice, germination and seedling development can progress in both the presence and absence of oxygen. While the transcriptomic responses to anaerobic conditions, found using microarrays, have revealed common responses, even across kingdoms, these alone are not sufficient for altering tolerance to anaerobic conditions. An in-depth study was undertaken which resulted in data creation from several time points during germination and in the rice coleoptile using RNA-seq analyses.

Created: 2016

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Other Information
Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation

doi : 10.1111/tpj.13418

Article Citation: Narsai, R., Secco, D., Schultz, M. D., Ecker, J. R., Lister, R. and Whelan, J. (2017), Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. Plant J, 89: 805–824. doi:10.1111/tpj.13418

La Trobe University Genomics Platform

uri : http://www.latrobe.edu.au/genomics

The La Trobe University Genomics Platform provides investigators with the latest in next-generation sequencing equipment and complementary bioinformatics assistance. We facilitate wide-ranging research projects requiring highly detailed global DNA and RNA sequence analysis. The Genomics Platform is part of the La Trobe Research Platforms and is available to investigators both internal and external to La Trobe University.

La Trobe University RNAseq Database

doi : 10.4225/22/592fa09c2f852

Identifiers