TRANS PROF DB: A new resource for sharing translational profiles.
Bottom Line: Results are provided at the level of an annotated conclusion for each gene, e.g. "Translation up-regulated", and also, where available, in a rawer form such as the normalized analyzed microarray output.We encourage all researchers to deposit their translational profiling data into TRANS PROF DB to enable us to create a truly comprehensive resource.TRANS PROF DB is available without restriction at mrctools.mrctox.le.ac.uk/TRANS_PROF_DB.
Affiliation: MRC Toxicology Unit ; Leicester, UK.
The translational efficiency of individual mRNAs can be measured on a genome-wide scale using translational profiling techniques. Data from such experiments are an enormously important resource in the quest to understand the impact of cellular state on gene expression. To improve our understanding of these data, we have created TRANS PROF DB, a manually curated resource containing the translational status of human mRNAs under defined conditions. Results are provided at the level of an annotated conclusion for each gene, e.g. "Translation up-regulated", and also, where available, in a rawer form such as the normalized analyzed microarray output. TRANS PROF DB aims to provide a central resource for the sharing of translational profiles to facilitate reuse of published data and to enable meta-analyses across data sets. As the database expands, it will provide an easily searchable archive of publicly available translational profiling data sets. We encourage all researchers to deposit their translational profiling data into TRANS PROF DB to enable us to create a truly comprehensive resource. TRANS PROF DB is available without restriction at mrctools.mrctox.le.ac.uk/TRANS_PROF_DB.
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Related in: MedlinePlus
Mentions: For a detailed description of the polysome profiling and microarray analysis techniques used to generate translational profiles, please see Melamed & Arava.12 For a laboratory protocol for performing polysome profiling please see the TRANS PROF DB website. Briefly (see Fig. 2); cycloheximide is used to arrest the elongation step of translation and fix the ribosomes in position on the mRNA, a sucrose gradient is used to separate the mRNA according to the number of ribosomes attached, RNA is purified from fractions of the gradient, and labelled cDNA is generated and hybridized to a microarray slide. Subsequent analysis of the slides from control and treated samples provides a measure of how the relative number of ribosomes attached to specific mRNAs has been affected by the treatment, and therefore, with assumptions, how the translation rate of specific mRNAs has changed. For a detailed protocol for the ribosome profiling technique please see Ingolia.13 In brief; cells are treated with cycloheximide to arrest the ribosomes on the mRNAs, a post nuclear lysate is obtained and digested with RNase I before ribosome protected fragments (RPFs) are recovered by size selection and used to generate sequencing libraries. Total mRNA samples are extracted and sequenced at the same time. The ratio of RPFs to total mRNA can then be used to detect changes in the translational efficiency of individual genes in the condition under investigation, compared to the control.Figure 2.
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