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The Yeast Resource Center Public Data Repository

M. Riffle
2004 Nucleic Acids Research  
The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's  ...  The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure  ...  ACKNOWLEDGEMENTS This work is supported by the National Center for Research Resources of the National Institutes of Health by a grant to T.N.D. entitled 'Comprehensive Biology: Exploiting the Yeast Genome  ... 
doi:10.1093/nar/gki073 pmid:15608220 pmcid:PMC540027 fatcat:uz6qbo4h4razvohcsu53gn7fkm

Proteomics data repositories

Michael Riffle, Jimmy K. Eng
2009 Proteomics  
The resources chosen reflect a current "snapshot" of the state of resources available with an emphasis placed on resources that may be of particular interest to yeast researchers.  ...  To facilitate the dissemination of these data, centralized data repositories have been developed that make the data and results accessible to proteomics researchers and biologists alike.  ...  Acknowledgments This work is supported by the University of Washington's Proteomics Resource (UWPR95794) and the National Center for Research Resources of the National Institutes of Health (P41 RR11823  ... 
doi:10.1002/pmic.200900216 pmid:19795424 pmcid:PMC2908408 fatcat:w6drphet6rd6nk3uvzu7d2dnj4

Navigating Public Microarray Databases

Christopher J. Penkett, Jürg Bähler
2004 Comparative and Functional Genomics  
Here we provide a guide to the use of these public microarray resources.  ...  The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide  ...  We also thank Matloob Qureshi for supplying the script that creates ADF files for our arrays, and Rob Andrews, Philippe Rocca-Serra and Helen Parkinson for their help with our data submissions to ArrayExpress  ... 
doi:10.1002/cfg.427 pmid:18629145 pmcid:PMC2447434 fatcat:d7gmuubz45fqlaqs3jaukkdaj4

The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images

Michael Riffle, Trisha N Davis
2010 BMC Bioinformatics  
Description: The Yeast Resource Center Public Image Repository (YRC PIR) is a large database of images depicting the subcellular localization and colocalization of proteins.  ...  All images and associated data are searchable, and the results browsable, through an intuitive web interface.  ...  Acknowledgements This work was supported by the National Center for Research Resources (P41RR11823 to TND) and the National Institute of General Medical Sciences (R01GM40506 to TND). Author Details  ... 
doi:10.1186/1471-2105-11-263 pmid:20482811 pmcid:PMC2882934 fatcat:lxpwwuvswzakpk4xgaflmiwr54

Meeting report: 2nd workshop of the United States culture collection network (May 19–21, 2014, State College, PA, USA)

Kevin McCluskey, Scott Bates, Kyria Boundy-Mills, Arianna Broggiato, Anthony Cova, Philippe Desmeth, Chobi DebRoy, Deborah Fravel, George Garrity, María del Mar Jiménez Gasco, Lucy Joseph, Daniel Lindner (+8 others)
2014 Standards in Genomic Sciences  
International Culture Collection of (Vesicular) Arbuscular Mycorrhizal Fungi http://invam.wvu.edu/ National Center for Marine Algae and Microbiota https://ncma.bigelow.org/ Phaff Yeast Culture Collection  ...  Network for a Community of ex situ Microbial Germplasm Repositories.  ...  Acknowledgements The RCN for a community of ex situ microbial germplasm repositories is supported by grant # 1203112 from the US National Science Foundation Division of Biological Infrastructure.  ... 
doi:10.1186/1944-3277-9-27 fatcat:2qlf7xwmenga3ioxlflkrvcxb4

The challenges faced by living stock collections in the USA

Kevin McCluskey, Kyria Boundy-Mills, Greg Dye, Erin Ehmke, Gregg F Gunnell, Hippokratis Kiaris, Maxi Polihronakis Richmond, Anne D Yoder, Daniel R Zeigler, Sarah Zehr, Erich Grotewold
2017 eLife  
Here, we review some of the contributions made by living stock collections to research across all branches of the tree of life, and outline the challenges they face.  ...  These collections provide a uniform and stable supply of living organisms and related materials that enhance the reproducibility of research and minimize the need for repetitive calibration.  ...  Acknowledgements 306 Many of the ideas presented here were formalized during an NSF-supported workshop on the 307 power of biological infrastructure to advance knowledge (DBI-1642534 to ADY).  ... 
doi:10.7554/elife.24611 pmid:28266913 pmcid:PMC5376150 fatcat:2znvu5tuljawdjt2lwan6kwvrq

DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research

Catherine Y. Seiler, Jin G. Park, Amit Sharma, Preston Hunter, Padmini Surapaneni, Casey Sedillo, James Field, Rhys Algar, Andrea Price, Jason Steel, Andrea Throop, Michael Fiacco (+1 others)
2013 Nucleic Acids Research  
The mission of the DNASU Plasmid Repository is to accelerate research by providing high-quality, annotated plasmid samples and online plasmid resources to the research community through the curated DNASU  ...  Plasmids can be requested directly through the DNASU website. DNASU and the PSI:Biology-Materials Repositories were previously described in the 2010 NAR Database Issue (  ...  Most especially, we want to thank the PSI:Biology centers, the PSI:Biology Structural Biology Knowledgebase, and the NIGMS staff for their continued support and input in all aspects of this project.  ... 
doi:10.1093/nar/gkt1060 pmid:24225319 pmcid:PMC3964992 fatcat:pilvjj7kq5hj3c65tpjwi445ye

EpoDB: An erythropoiesis gene expression database in progress [chapter]

Fidel Salas, Juergen Haas, Christian J. Stoeckert, G. Christian Overton
1996 Lecture Notes in Computer Science  
For yeast the website http://www.yeastgenome.org lists the following resources: - The list for repositories gives an idea of a significant but manageable number of repositories maintained in the world  ...  data collection and repository site for designed parts.  ... 
doi:10.1007/bfb0033203 fatcat:ltcxl5dva5ecxik7tati4wy6bm

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

R. Edgar
2002 Nucleic Acids Research  
The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data.  ...  A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.  ...  Gavin Sherlock when making data submissions.  ... 
doi:10.1093/nar/30.1.207 pmid:11752295 pmcid:PMC99122 fatcat:kkqxtbylqneufa7nlqn5z6xllm

FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update

Yanhui Hu, Aram Comjean, Charles Roesel, Arunachalam Vinayagam, Ian Flockhart, Jonathan Zirin, Lizabeth Perkins, Norbert Perrimon, Stephanie E. Mohr
2016 Nucleic Acids Research  
) serve as a reagent production tracking system, screen data repository, and portal to the community.  ...  The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu  ...  Their critical feedback and open sharing have helped us to improve the resources and data we provide to the community.  ... 
doi:10.1093/nar/gkw977 pmid:27924039 pmcid:PMC5210654 fatcat:zfht7ymfxrcydhtm7u4h646nse

A Review of Living Collections with Special Emphasis on Sustainability and Its Impact on Research Across Multiple Disciplines

Kevin McCluskey
2017 Biopreservation and Biobanking  
Comprising diverse resources, microbe culture collections, crop and biodiversity plant germplasm collections, and animal germplasm repositories are commonly allied with specific research communities or  ...  International treaty obligations and restrictions on release of genetically modified organisms complicate the activities of living collections.  ...  Acknowledgments This is contribution No. 16-365-J from the Kansas Agricultural Experiment Station. Partial support for publication charges was provided by grant DBI 1534564 from the U.S.  ... 
doi:10.1089/bio.2016.0066 pmid:27869477 pmcid:PMC5327032 fatcat:v6d2j2r335dzdpehgb7evzmsq4

The U.S. Culture Collection Network Lays the Foundation for Progress in Preservation of Valuable Microbial Resources

Kevin McCluskey, Anne Alvarez, Rick Bennett, Deepak Bokati, Kyria Boundy-Mills, Daniel Brown, Carolee T. Bull, Michael Coffey, Tyler Dreaden, Clifford Duke, Greg Dye, Erin Ehmke (+28 others)
2016 Phytopathology  
All of the collections with backup at the NCGRP are public distributing collections including U.S. NSF-supported genetic stock centers, USDA-ARS collections, and university-supported collections.  ...  The meeting allowed collection curators who had already backed up their resources at the USDA NCGRP to visit the site, and brought collection owners, managers, and stakeholders together.  ...  This is publication number 16-171-J of the Kansas Agricultural Experiment Station.  ... 
doi:10.1094/phyto-02-16-0074-rvw pmid:26976729 fatcat:6bnkc7iwdnbpvkiden6ckkrarm

Endocrine-Related Resources from the National Institutes of Health

2008 Endocrinology  
NCRR -Various Cell Repositories NCRR maintains the following cell repository resources: National Cell Culture Center, National Stem Cell Resource, and the Yeast Genetic Stock Center.  ...  NCRR -Mutant Mouse Regional Resource Centers (MMRRC) The Mutant Mouse Regional Resource Center (MMRRC) Program consists of centers that collectively operate as a one-stop shop to serve the biomedical research  ... 
doi:10.1210/endo.149.4.9997 fatcat:3i6frmyosbgl5eaeuxzwb4lupq

Endocrine-Related Resources from the National Institutes of Health

2008 Molecular Endocrinology  
Funded by grants through NCRR's Division of Comparative Medicine (DCM), each center, staffed with experienced research and support staff, provides the appropriate research environment to foster the development  ...  Further information may be obtained from the notice, Procedures for Accessing Regional Primate Research Centers, published in the NIH Guide for Grants and Contracts at http://grants2.nih.gov/grants/guide  ...  NIA -Aging Cell Bank NCRR -Various Cell Repositories NCRR maintains the following cell repository resources: National Cell Culture Center, National Stem Cell Resource, and the Yeast Genetic Stock Center  ... 
doi:10.1210/mend.22.6.9999 pmid:18511499 pmcid:PMC5419538 fatcat:lh4jwjsutjgb3n7d3a4ybcoalq

Endocrine-Related Resources from the National Institutes of Health

2008 Endocrinology  
Specimens are collected according to the investigator's individual protocol. Information provided with the specimens includes routine histopathologic and demographic data.  ...  The NCI Cooperative Human Tissue Network (CHTN) provides normal, benign, precancerous, and cancerous human tissue to the scientific community for biomedical research.  ...  NCRR -Various Cell Repositories NCRR maintains the following cell repository resources: National Cell Culture Center, National Stem Cell Resource, and the Yeast Genetic Stock Center.  ... 
doi:10.1210/endo.149.8.9996 fatcat:aqh7cwtronaofh2bgvyfbyt6vi
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