07/16/08

• The 3.0 version of the Model Genome Interrogator has been released. Credits: Lu, H., N. Lauter, E. Cannon, S. Dash, D. Hessel, M. Moscou, R. Wise, J. Dickerson, V. Brendel

04/21/08

• We are pleased to announce the release of our newest Affymetrix GeneChip page for cotton. PLEXdb now provides annotation information for cotton along with access to all of its statistical and visualization tools. We will be happy to receive your cotton GeneChip data as a common resource for the cotton and greater plant communities.

03/24/08

• New Experiments Released:
  • BB49 : A 'Barley stem rust interaction' experiment from Dr. A. Kleinhofs. This data set supports the publication: Parallel expression profiling of barley�stem rust interactions. Zhang L, Castell-Miller C, Dahl S, Steffenson B, Kleinhofs A. Funct Integr Genomics (2008, Jan 15, epub ahead of print)
    
    
  • BB53 : Another Barley dat set, 'Functional Genomic Analysis Of Barley(Hordeum vulgare L.) Grain Protein Accumulation' and the corresponding publication is: Aravind K. Jukanti, Nancy M. Heidlebaugh, David L. Parrott, Isabelle A. Fischer, Kate McInnerney and Andreas M. Fischer. Comparative transcriptome profiling of near-isogenic barley (Hordeum vulgare) lines differing in the allelic state of a major grain protein content locus identifies genes with possible roles in leaf senescence and nitrogen reallocation. New Phytologist 177(2):333-349 (Jan 2008).

02/27/08

• New Experiments Released:
  • GM3 : Expression patterns in time and space during P.sojae infection of soybean cultivars differing in quantitative resistance. A large soybean-pathogen dat set released from Brett Tyler(Bruno Sobral).
    
    
  • FG7 : Another Fusarium data set from Dr.Gary Muehlbauer: Fusarium gene expression profiles during conidia germination stages. Please see their publication: Seong KY, Zhao X, Xu JR, G�ldener U, Kistler HC. Conidial germination in the filamentous fungus Fusarium graminearum. Fungal Genetics and Biology (2007 Sep 14).
    
    
  • TA9 : The first wheat-pathogen experiment in PLEXdb, TA9, has been released from Dr. Xianming Chen's lab. This data set supports the publication: TRISTAN E. CORAM, MEINAN WANG AND XIANMING CHEN. Transcriptome analysis of the wheat�Puccinia striiformis f. sp. tritici interaction. MOLECULAR PLANT PATHOLOGY 9 (2): 157-169 (2008).

2/21/08

• The PLEXdb Software Workshop presentation for PAG XVI, 2008 is now available as a PDF.

1/2/08

• Soybean experiment GM2 released: 'Distinct biphasic mRNA changes in response to Asian soybean rust infection', van de Mortel M, Recknor JC, Graham MA, Nettleton D, Dittman JD, Nelson RT, Godoy CV, Abdelnoor RV, Almeida AM, Baum TJ, Whitham SA

11/13/07

• Annotation for Rice Array long oligo 45k microarray completed. The new annotation page covers probes on both the 20k and 45k arrays.

10/24/07

• PLEXdb 2.0 has been released. New features include:
  • new server with significantly more storage (Sun X4600 Server with 4 dual core CPU's and 16GB of memory and a Sun SE6140 disk array with 8TB of data storage).
  • PLEX Express, the new experiment submission process, and a revised normalization pipeline for processing expression data, which provides more visualizations and types of downloadable data.
  • updated database schema in keeping with MIAME/Plant recommendations.
  • new experiment navigation; all aspects of an experiment are accessible from one page.
  • all microarray annotation has been updated.

7/27/07

• A new PLEXdb tool for retrieving an annotation table for a list of probesets has been released.

7/1/07

• The new PLEXdb experiment processing pipeline has been completed. We have redesigned the experiment processing pipeline which runs RMA and MAS analysis on experiments after they have been finalized, generates a number of images and plots, and prepares files for download. The new pipeline is more rigorous and uses the latest analysis tools from Bioconductor and Affymetrix.

6/27/07

• VV3 released: 'Tissue-specific mRNA expression profiling in grape berry tissues', Grimplet J, Deluc LG, Tillett RL, Wheatley MD, Schlauch KA, Cramer GR, Cushman JC, BMC Genomics. 2007 Jun 21;8(1):187

6/22/07

• VV7 released: 'Gene expression associated with compatible viral diseases in grapevine cultivars', Espinoza C, Vega A, Medina C, Schlauch K, Cramer G, Arce-Johnson P, Funct Integr Genomics 2007 Apr;7(2):95-110. Epub 2006 Jun 15

10/31/06

• Experiment BB28 released. This experiment corresponds to the publication, 'Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley'. L. Zhang, T. Fetch, J. Nirmala, D. Schmierer, R. Brueggeman, B. Steffenson and A. Kleinhofs

9/15/06

• New publication of meta-analysis of barley-powdery mildew interactions: Caldo RA, D Nettleton, J Peng, and RP Wise. 2006. Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles. Molecular Plant-Microbe Interactions 19(9): 939-947. Supports accession BB4 and BB2

07/10/06

• The publication 'Genetic diversity contribution to errors in short oligonucleotide microarray analysis', Kirst M, Caldo R, Casati P, Tanimoto G, Walbot V, Wise RP, and Buckler ES has been published in Plant Biotechnology Journal. The data set ZM1 is ovailable here.