Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression ATLAS of Brachypodium distachyon (cv. BD21) during photomorphogenesis (transition from dark to light)

ABSTRACT: Brachypodium, also called as Purple False Brome, a bioenergy crop model is related to grasses and major cereal grain species especially Triticeae (wheat, barley, etc.). It's small genome size, a short life cycle, and few growth requirements make this plant as a model for functional genomics studies. At the time of germination, the exposure to light may play an important role in the early development of the seedling. In order to explore transcriptional programs and genes operating in dark and light conditions, an RNA-Seq based study of 6 libraries prepared from poly-A rich mRNA fraction was carried out. For each treatment type dark and light, three individual plants were used as biological replicates.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Brachypodium distachyon

SUBMITTER: Pankaj Jaiswal

PROVIDER: E-MTAB-6445 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC). The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Series 1: Growth conditions: Sterilized seeds will be stratified at 4degreeC for 3 days, exposed to white light for 2 h to induce germination, and grown on MS agar plates (0.9 % agar) without sugar in total darkness for 4 days at 22degreeC. Seedlings will then be transferred to the light conditions described for each slide below for 1 h (to identify early induced genes) and 4 hrs (maximum expression of the first initial light response of most target genes), respectively. All light treatments will be done in parallel to minimize the number of dark controls. All samples will be done in triplicate and only with shoots. Experimenter name = Thomas Kretsch; Experimenter institute = AtGenExpress Experiment Overall Design: 48 samples were used in this experiment

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Gene expression ATLAS of Brachypodium distachyon (cv. BD21) during photomorphogenesis (transition from dark to light)

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