03/31/09

• New Barley Experiments Released:
• BB63 : Late response to boron toxicity in barley leaves. The associated publication is: Microarray Analysis of Late Response to Boron Toxicity in Barley (Hordeum vulgare L.) Leaves. Turkish Journal of Agriculture and Forestry, 33: 191-202, 2009.
  BB63 has also been submitted at GEO via PLEXdb, GSE14521.
  
  
• BB20 : Genotype-dependent gene expression in barley. From Arnis Druka's group.
  
  
• BB21 : Genetics of gene expression in barley. This data set supports two of their publications:
  'Gene expression quantitative trait locus analysis of 16000 barley genes reveals a complex pattern of genome-wide transcriptional regulation'. Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M. The Plant Journal. 2007 Oct 18.
  'SFP Genotyping From Affymetrix Arrays Is Robust But Largely Detects Cis-acting Expression Regulators', Z. W. Luo, E. Potokina, A. Druka, R. Wise, R. Waugh and M. J. Kearsey Genetics, Vol. 176, 789-800, June 2007.

01/22/09

• BB10: A Barley pathogenesis experiment on powdery mildew has been released from Roger Wise's group. This data set is associated with their publication: 'Blufensin1 negatively impacts Basal defense in response to barley powdery mildew'. Meng Y, Moscou MJ, Wise RP. 2009(Jan). Plant Physiol. 149(1):271-85.

12/24/08

• Gene OscilloScope:   A new tool at PLEXdb to find out in which experiment your favorite gene does something interesting !
  Given a probe set, it searches for experiments where the expression of a queried gene fluctuates (oscillates) the most. The result displays the extent of fluctuation (CV) of the treatment means in each of the experiments visible to the user.

11/19/08

• Medicago Gene Expression Atlas: ME1 from Michael Udvardi's lab is now in PLEXdb and is a useful addition to our other gene expression atlas experiments in wheat, barley and Arabidopsis. It supports the publication: A gene expression atlas of the model legume Medicago truncatula. Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, Moreau S, Niebel A, Frickey T, Weiller G, He J, Dai X, Zhao PX, Tang Y, Udvardi MK. Plant J. 2008 Aug;55(3):504-13. Epub 2008 Apr 12.

10/09/08

• Submission at GEO via PLEXdb: PLEXdb has already submitted 7 experiments at GEO on behalf of the original submitters: 3 of these are public and 4 are private at GEO. You are welcome to take advantage of this facility. Two birds in one shot: Submit your data once, at PLEXdb, and with your consent we deposit it at NCBI-GEO. You always have the choice to keep it private at GEO.
  
  
• Annotation: Microarray annotation has been updated to TAIR 8 and the August, 2008 release of UniProt uniref90 sequence.

09/17/08

• Expression Atlas of Arabidopsis Development (from AtGenExpress), AT40 can now be accessed at PLEXdb. The accession AT40 compares the expression of 63 tissues from wildtype Columbia. It's accompanying accession AT41 includes a few developmental mutants along with the corresponding WT controls.
  
  
• AT31:A pathogenicity experiment in Arabdopsis has now been made publicly visible by Michael Krogh Jensen, University of Copenahgen. AT31 data set relates to their publication: Transcriptional regulation by a NAC (NAM-ATAF1,2-CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f.sp. hordei in Arabidopsis., Jensen MK, Hagedorn PH, de Torres-Zabala M, Grant MR, Rung JH, Collinge DB, Lyngkjaer MF. Plant J. 2008 Aug 6. [Epub ahead of print]

09/04/08

• Two tools have been added to PLEXdb.
  • The Microarray Platform Translator (MPT) has been re-designed and re-implemented from its predecessor in BarleyBase.
  • The GO annotator retrieves GO annotation for one or more probe set ids.

08/25/08

• TA3 - Wheat Gene Atlas released. Thirteen developmental stages from seed to seed: From Andreas Schreiber, Ute Baumann, Tim Sutton, Roger Wise, Gary Muehlbauer, Robbie Waugh and Peter Langridge.

07/31/08

• A wheat P.s. tritici infection experiment, TA11 has now been released courtesy of Dr. TE Coram. This data supports their publication: Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat-Puccinia striiformis f. sp. tritici interaction. TRISTAN E. CORAM, MATTHEW L. SETTLES AND XIANMING CHEN. MOLECULAR PLANT PATHOLOGY (2008) 9(4), 479-493

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.