TraVA


30813912	An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana. [PMID: 30813912] Klepikova AV, Kulakovskiy IV, Kasianov AS, Logacheva MD, Penin AA. Abstract BACKGROUND:Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. RESULTS:The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. CONCLUSIONS:Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress . BMC Plant Biol. 2019:19(Suppl 1) \| 11 Citations (from Europe PMC, 2025-03-22)
27549386	A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. [PMID: 27549386] Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA. Abstract Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing. The expression of 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open-access web-based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages. Plant J. 2016:88(6) \| 362 Citations (from Europe PMC, 2025-03-22)

An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana. [PMID: 30813912]

Klepikova AV, Kulakovskiy IV, Kasianov AS, Logacheva MD, Penin AA.

BACKGROUND:Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. RESULTS:The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. CONCLUSIONS:Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress .

BMC Plant Biol. 2019:19(Suppl 1) | 11 Citations (from Europe PMC, 2025-03-22)

A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. [PMID: 27549386]

Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA.

Abstract

Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing. The expression of 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open-access web-based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages.

Plant J. 2016:88(6) | 362 Citations (from Europe PMC, 2025-03-22)

URL:	http://travadb.org
Full name:	TRAnscriptome Variation Analysis
Description:	TraVA, is the database of gene expression profiles in Arabidopsis thaliana based on RNA-seq analysis. Currently, profiles of 25706 protein-coding genes in 79 samples are presented. It allows visualization and analysis of gene expression profiles and differential gene expression between organs using two of the most reliable and widely accepted statistical approaches, DESeq/DESeq2 and BaySeq .
Year founded:	2016
Last update:
Version:
Accessibility:	Accessible
Country/Region:	Russian Federation

Data type:	DNA
Data object:	Plant
Database category:	Expression Raw bio-data
Major species:	Arabidopsis thaliana
Keywords:	transcriptome RNA-seq alternative splicing transcription factor

University/Institution:	Lomonosov Moscow State University
Address:	A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
City:	Moscow
Province/State:
Country/Region:	Russian Federation
Contact name (PI/Team):	Aleksey A. Penin
Contact email (PI/Helpdesk):	alekseypenin@gmail.com

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Database Commons a catalog of worldwide biological databases