title: A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling.
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.
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Klepikova
authors.affiliation: A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Artem S
authors.initials: AS
authors.lastname: Kasianov
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia.|Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Evgeny S
authors.initials: ES
authors.lastname: Gerasimov
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia.|A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|Laboratory of Extreme Biology, Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Logacheva
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia.|A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Aleksey A
authors.initials: AA
authors.lastname: Penin
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors
keywords: 
  Arabidopsis thaliana
  ; RNA-seq; alternative splicing; differentially expressed genes; gene expression analysis; transcription factor