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Cells respond to stress by remodeling their transcriptome through transcription and degradation. Xrn1p-dependent degradation in P-bodies is the most prevalent decay pathway, yet, P-bodies may facilitate not only decay, but also act as a storage compartment. However, which and how mRNAs are selected into different degradation pathways and what determines the fate of any given mRNA in P-bodies remain largely unknown. We devised a new method to identify both common and stress-specific mRNA subsets associated with P-bodies. mRNAs targeted for degradation to P-bodies, decayed with different kinetics. Moreover, the localization of a specific set of mRNAs to P-bodies under glucose deprivation was obligatory to prevent decay. Depending on its client mRNA, the RNA-binding protein Puf5p either promoted or inhibited decay. Furthermore, the Puf5p-dependent storage of a subset of mRNAs in P-bodies under glucose starvation may be beneficial with respect to chronological lifespan.
Pubmed ID: 29297464 RIS Download
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A commercial antibody supplier and provider of various services.
View all literature mentionsNon-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.
View all literature mentionsA division of Applied Biosystems selling products for the isolation, detection, quantification, amplification, and characterization of RNA.
View all literature mentionsCommercial instrument and chemical vendor. Developer and manufacturer of specialized technological products for life science research and clinical diagnostics markets.
View all literature mentionsCommercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
View all literature mentionsA contract research organization providing drug development and animal testing services. Under the name Covance Research Products Inc., based in Denver, Pennsylvania, the company also deals in the import, breeding and sale of laboratory animals. It breeds dogs, rabbits, guinea pigs, non-human primates, and pigs, and runs the largest non-human primate laboratory in Germany. (Wikipedia)
View all literature mentionsCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsThis unknown targets
View all literature mentionsThis monoclonal targets Yeast 3-phosphoglycerate kinase (PGK)
View all literature mentionsThis monoclonal targets c-Myc
View all literature mentionsThis polyclonal secondary targets IgG (H+L)
View all literature mentionsThis polyclonal targets Digoxigenin
View all literature mentionsFunctional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.
View all literature mentionsImaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition.
View all literature mentionsDigital image processing system where microscope settings and processing steps may be adjusted in single user interface. Can acquire images from variety of cameras. Includes software package for capturing, archiving and preparing images for publication. Allows users to visualize and present images in several dimensions. Functionality of imaging toolbox expands constantly with wide range of different modules that are tailored to specific applications or microscope accessories. This resource is duplicated by SCR_018376
View all literature mentionsSoftware repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
View all literature mentionsOpen source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsGOstat is a tool that allows you to find statistically overrepresented Gene Ontologies within a group of genes. The Gene-Ontology database (GO: http://www.geneontology.org) provides a useful tool to annotate and analyze the function of large numbers of genes. Modern experimental techniques, as e.g. DNA microarrays, often result in long lists of genes. To learn about the biology in this kind of data it is desirable to find functional annotation or Gene-Ontology groups which are highly represented in the data. This program (GOstat) should help in the analysis of such lists and will provide statistics about the GO terms contained in the data and sort the GO annotations giving the most representative GO terms first. Run GOstat: * Go to search form - Computes GO statistics of a list of genes selected from a microarray. * GOstat Display - You can store results from a previously run and view them here, either by uploading them as a file or putting them on a selected URL. * Upload Custom GO Annotations - This allows you to upload your own GO annotation database and use it with GOstat. Variants of GOstat: * Rank GOstat - Takes input from all genes on microarray instead of using a fixed cutoff and uses ranks using a Wilcoxon test or either ranks or pvalues to score GOs using Kolmogorov-Smirnov statistics. * Gene Abundance GOstats - Takes input from all genes on microarray and sums up the gene abundances for each GO to compute statistics. * Two list GOstat - Compares GO statistics in two independent lists of genes, not necessarily one of them being the complete list the other list is sampled from. Platform: Online tool
View all literature mentionsBioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
View all literature mentionsScript distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data.
View all literature mentionsSoftware ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
View all literature mentionsSoftware Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
View all literature mentionsFunctional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.
View all literature mentionsImaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition.
View all literature mentionsDigital image processing system where microscope settings and processing steps may be adjusted in single user interface. Can acquire images from variety of cameras. Includes software package for capturing, archiving and preparing images for publication. Allows users to visualize and present images in several dimensions. Functionality of imaging toolbox expands constantly with wide range of different modules that are tailored to specific applications or microscope accessories. This resource is duplicated by SCR_018376
View all literature mentionsSoftware repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
View all literature mentionsOpen source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsGOstat is a tool that allows you to find statistically overrepresented Gene Ontologies within a group of genes. The Gene-Ontology database (GO: http://www.geneontology.org) provides a useful tool to annotate and analyze the function of large numbers of genes. Modern experimental techniques, as e.g. DNA microarrays, often result in long lists of genes. To learn about the biology in this kind of data it is desirable to find functional annotation or Gene-Ontology groups which are highly represented in the data. This program (GOstat) should help in the analysis of such lists and will provide statistics about the GO terms contained in the data and sort the GO annotations giving the most representative GO terms first. Run GOstat: * Go to search form - Computes GO statistics of a list of genes selected from a microarray. * GOstat Display - You can store results from a previously run and view them here, either by uploading them as a file or putting them on a selected URL. * Upload Custom GO Annotations - This allows you to upload your own GO annotation database and use it with GOstat. Variants of GOstat: * Rank GOstat - Takes input from all genes on microarray instead of using a fixed cutoff and uses ranks using a Wilcoxon test or either ranks or pvalues to score GOs using Kolmogorov-Smirnov statistics. * Gene Abundance GOstats - Takes input from all genes on microarray and sums up the gene abundances for each GO to compute statistics. * Two list GOstat - Compares GO statistics in two independent lists of genes, not necessarily one of them being the complete list the other list is sampled from. Platform: Online tool
View all literature mentionsBioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
View all literature mentionsScript distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data.
View all literature mentionsSoftware ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
View all literature mentionsSoftware Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
View all literature mentionsThis monoclonal targets Yeast 3-phosphoglycerate kinase (PGK)
View all literature mentionsThis monoclonal targets c-Myc
View all literature mentionsThis unknown targets
View all literature mentionsThis polyclonal secondary targets IgG (H+L)
View all literature mentionsThis unknown targets
View all literature mentionsThis polyclonal targets Digoxigenin
View all literature mentionsThis monoclonal targets Yeast 3-phosphoglycerate kinase (PGK)
View all literature mentionsThis monoclonal targets c-Myc
View all literature mentionsThis polyclonal secondary targets IgG (H+L)
View all literature mentionsThis unknown targets
View all literature mentionsThis polyclonal targets Digoxigenin
View all literature mentionsThis monoclonal targets Yeast 3-phosphoglycerate kinase (PGK)
View all literature mentionsThis monoclonal targets c-Myc
View all literature mentionsThis polyclonal secondary targets IgG (H+L)
View all literature mentionsThis unknown targets
View all literature mentionsThis polyclonal targets Digoxigenin
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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