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What's New

Note: Funding for this project ended on September 30, 2007. This site will maintained for the near future. Arrays can still be ordered through the website and are still being printed at the University of California-Davis facility. Please direct all inquires to: Pam Ronald and Janice Pfeiff regarding availability of the arrays. If there are problems with the website, please email ricearray at TIGR.


March 13, 2007

  • Oligos from the 20K and 45K rice array have been mapped to the latest release (release 5) of the TIGR Rice Genome Annotation project.


    • November 2, 2006

  • The experiment performed to validate the 45K array design is available as a pdf for download in the Array Validation section.


    • September 25, 2006

  • Position closed: TIGR is no longer accepting applications for the the Bioinformatics Engineer position in the Plant Genomics group. We thank all the applicants who expressed interest in this opportunity.


    • August 22, 2006

  • NCBI Gene Expression Omnibus platform accessions have been assigned to the 45K (23K A + B) array. Visit the GEO Submission Page for more details.


    • August 21, 2006

  • Oligo annotations for the Rice 45K and Rice 20K array oligos have been updated. New annotation includes mappings to the TIGR Plant Transcript Assemblies and full length cDNAs.
  • Added oligos from other array platform (Affymetrix, Agilent and Yale/BGI) to the oligo database.


    • August 10, 2006

  • The Rice Oligonucleotide Array project array 45k (23k x 2) oligos are available for searching using the Basic, Advanced or Batch searches.
  • The Rice Oligonucleotide Array project array 45k (23k x 2) and 20k oligos have been remapped to the TIGR Rice Genome Project release 4 annotation, full length cDNAs and TIGR Plant Transcript Assemblies.


    • June 15, 2006

  • The Rice Oligonucleotide Array project website will be unavailable July 1-4, 2006 due to scheduled server maintenance.
  • Rice 20k and 45k GenePix Array List (GAL) files have been updated in the Rice Layout pages.


    • June 8, 2006

  • The Rice Multi-platform Microarrary Search file has been updated. The latest version is dated June 6th, 2006. Visit the Rice Multi-platform Microarrary Search to download.


    • June 7, 2006

  • Position opening: TIGR is seeking qualified applicants for a Bioinformatics Engineer position within the Plant Genomics Department. For a detailed description of what the position entails, requirements, and how to apply, visit the Project Openings page.


    • May 2, 2006

  • GenePix Array List (GAL) files for the new 45K array is available for download from the Array Layout page. Since the 45K array is distributed as a set of two 23K arrays, each array requires their own separate GAL (A + B). The annotation for the oligos on each GAL include mappings to release 4 TIGR Rice Genome Annotation, EST abundance, TIGR Plant Transcript Assemblies for rice, full length cDNAs, and GO terms.


    • April 24, 2006

  • A FAQ discussing common issues concerning printing and proper handling and usage of the arrays is available at Array Handling and Printing FAQ.


    • April 14, 2006

  • The Rice Multi-platform Microarray Search page has been updated with probe mappings to the TIGR Rice Genome Annotation v4 release loci and TIGR Plant Transcript Assemblies.


    • March 22, 2006

  • The rice 45K array is available as a set of 2 23K arrays. To place an order for your arrays, visit the Order Arrays page. Each set of 2 23K arrays is $110.


    • February 28, 2006

  • A description of the process used to validate the 20K array design is available in a new Array Validation page.


    • February 22, 2006

  • The GenePix Array Layout (GAL) for the forthcoming 45K array is available in the Array Layout section. Each oligo on the array has been mapped to release 4 TIGR rice genome annotations if possible, and to other databases (full length cDNAs, transcript assemblies, NRAA and pseudomolecules) if mappings at 100% identity at 100% length exist.


    • February 9, 2006

  • The UCDavis ArrayCore Facility is now setting up a full service facility for labelling and hybridizations. Services will include mRNA isolation, labelling, scanning and image quantification. We are interested in seeking 1-2 beta users to test this service. For more information, visit the Hybridization Service page.
  • The oligo design for the new Xanthomonas oryzae array (4658 Xo oligos corresponding to 1000 oligos unique to Xanthomonas oryzae pv oryzae, 1000 oligos unique to Xanthomonas oryzae pv oryzicola and 2500 oligos shared between the 2 genomes) is now complete. Visit the Rice Array Project Home Page for more information on details and availability.


    • February 8, 2006

  • Due to a lack of a sufficient number of qualified applicants for the Microarray Hybridization and Analysis Workshop, the workshop has been cancelled. We thank all the applicants who applied and expressed interest in attending.


    • February 7, 2006

  • Position closed: TIGR is no longer accepting applications for the the Bioinformatics Analyst position. We thank all the applicants who expressed interest in this opportunity.


    • Januaray 9, 2006

  • The 45K array version to be released at the end of January 2006 will utilize a different slide chemistry from the 20K, requiring a different set of experimental protocols. Visit the updated Experimental Protocols page for more details.


    • December 22, 2005

  • Position opening: TIGR is seeking a qualified Bioinformatics Analyst to provide bioinformatic analyses and support to the project members. The position involves storage and processing of gene expression profiling data and annotation of the array elements. For more information and details on how to apply, visit the Rice Oligonucleotide Array Project Openings page.


    • December 21, 2005

  • From April 19-21 of 2006, TIGR will be hosting a microarray training workshop. For more information and details on how to apply, visit the Microarray Hybridization and Analysis Workshop page. Applications are due by January 22, 2006.


    • December 20, 2005

  • Basic, Advanced and Batch oligo searches now support querying for GO terms.
  • Rice Oligo Array (zip, 966K) table updated with GO terms.


    • December 9, 2005

  • Protocols updated.


    • December 5, 2005

  • The oligo design for the new 45K array (43,312 oligos corresponding to 44,974 TIGR V3 rice gene models) is now complete. The list of oligos may be downloaded here (zip, 967K). Anticipated release of the new array to the public will be in February '06. The cost per 45K array will be ~$110. Orders are now being accepted on the Order Arrays page.


    • November 18, 2005

  • New data release: Analysis of rice seedling expression (Affymetrix).


    • November 2, 2005

  • A FAQ describing Rice Oligonucleotide Array (ROMA) database expression data processing and loading methods is available.
  • The ROMA expression database is now online. One study comprising 72 hybs has been loaded into the database, Analysis of rice cellular expression (Tim Nelson). Two tools are provided for querying the database, a Study Search that allows queries on experiment title, description and factors and a Gene/Expression Search that allows queries for a set of genes/oligos.


    • October 12, 2005

  • An image showing a sample self-self hybridization using rice leaf RNA for the 20k array array is available in the Rice Status page.
  • We are accepting pre-orders for the 45k array which will be available in Novemeber. To reserve your 45K array, send an email specifying the quantity of arrays interested.


    • October 10, 2005

  • An order tracking page is now available for users who have purchased arrays and are interested in checking the status of their orders at any time. To apply for a username and password, email ricearray@tigr.org.


    • October 3, 2005

  • The ROMA database at TIGR is designed to support expression data from all publicly available rice array platforms including the NSF Rice Oligonucleotide Array Project, Agilent arrays, Affymetrix arrays, and the Yale/BGI oligonucleotide array. Please note that these publicly available data are available at other repositories such as the NCBI Gene Expression Omnibus and in the case of the Yale/BGI array, at the Virtual Center for Cellular Expression Profiling of Rice. Please note that we process the expression data using our methods and thus our normalized data may differ from that at other expression databases


    • September 19, 2005

  • The oligo design for the new 45k array (43483 oligos) is complete. Anticipated release of the new array to the public will be in fall '05. The cost per array will be ~ $220 for non-UC orders and $150 for UC affiliates. The exact price to be announced in October. Orders will be accepted in October on the Order Arrays page.


    • September 13, 2005

  • A new GPR metrics tool is available for array users that allows them to assess the quality of their hybridizations based on the GPR files generated. The tool calculates several array quality metrics such as total spots, percentage missing spots, percentage bad spots, and average foreground and background intensities across the different channels among other measures.


    • August 9, 2005

  • Two new tools are available to explore expression data: an Oligo and EST Anatomy Viewer to visualize maize transcriptome data and a Highly Expressed Gene Finder to identify genes that are highly expressed in certain tissues.




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    Last modified: Thursday, 01-Nov-2007 17:34:29 EDT