Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells
| Autor: | Yu-Ting Chen, Jian-Rong Li, Chun-Chi Liu, Chuan-Hu Sun |
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| Rok vydání: | 2018 |
| Předmět: |
Plant stress
0106 biological sciences 0301 basic medicine lcsh:QH426-470 lcsh:Biotechnology RNA-Seq Biology computer.software_genre Proteomics 01 natural sciences Database Transcriptome User-Computer Interface 03 medical and health sciences Differential expression Stress Physiological lcsh:TP248.13-248.65 Plant Cells Databases Genetic Genetics Abiotic component Molecular breeding RNA lcsh:Genetics 030104 developmental biology RNA Plant Identification (biology) DNA microarray computer Internet Access 010606 plant biology & botany Biotechnology |
| Zdroj: | BMC Genomics BMC Genomics, Vol 19, Iss 1, Pp 1-8 (2018) |
| ISSN: | 1471-2164 |
| Popis: | Background Abiotic and biotic stresses severely affect the growth and reproduction of plants and crops. Determining the critical molecular mechanisms and cellular processes in response to stresses will provide biological insight for addressing both climate change and food crises. RNA sequencing (RNA-Seq) is a revolutionary tool that has been used extensively in plant stress research. However, no existing large-scale RNA-Seq database has been designed to provide information on the stress-specific differentially expressed transcripts that occur across diverse plant species and various stresses. Results We have constructed a comprehensive database, the plant stress RNA-Seq nexus (PSRN), which includes 12 plant species, 26 plant-stress RNA-Seq datasets, and 937 samples. All samples are assigned to 133 stress-specific subsets, which are constructed into 254 subset pairs, a comparison between selected two subsets, for stress-specific differentially expressed transcript identification. Conclusions PSRN is an open resource for intuitive data exploration, providing expression profiles of coding-transcript/lncRNA and identifying which transcripts are differentially expressed between different stress-specific subsets, in order to support researchers generating new biological insights and hypotheses in molecular breeding or evolution. PSRN is freely available at http://syslab5.nchu.edu.tw/PSRN. Electronic supplementary material The online version of this article (10.1186/s12864-018-5367-5) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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