NASCArrays Information at The BAR

Welcome to NASCArrays information at the BAR. This page hosts meta-information from the NASCArrays service (2002-2013). This information was parsed from text files available on the NASCArrays site. NASCArrays data is on iPlant server. To download experiment data from iPlant, please click on the experiment number. To download the CEL files, please click on the ftp link.

Title:Transcriptome analysis of ARRESTED DEVELOPMENT 3 mutant.
Description:Aims: Comparison of transcriptome between mutant and wild-type plant. Based on the temperature sensitive period of the mutant the gene likely acts during the earliest stages of the specification of the leaf primordium. Background: The ARRESTED DEVELOPMENT 3 mutation causes a temperature dependent loss of all spongy mesophyll and most palisade parenchyma in developing leaves. Although these leaves lack most internal tissues excepting vasculature they continue to expand away from the main axis of plant growth. Mature leaves have a small midrib and marginal regions that are large balloons of epidermis covering airspace. add3 is a temperature sensitive mutation whose most severe phenotypic response occurs at a restrictive temperature of 29 degrees C.Using BAC and TAC filters a recombinant population we have generated and available and newly developed molecular markers a high resolution (1000 chromosomes scored) physical genetic map has been completed to define the physical extent of the locus. Transformation rescue and RNAi experiments are currently underway to determine if a candidate gene identified using the approach outlined above is ADD3. Experimentalia: Wild-type and add3 tissue will be grown at 29 degrees C until the first two true leaves have emerged. Two days after emergence the aerial portions of the plants will be collected and RNA will be isolated. This developmental stage will provide plants with primordia in various stages of development. The wild-type tissue will serve as a control for exposure of developing primordia to high temperature the add3 plants will provide the experimental transcriptome.We intend to use RNA isolation protocols provided by the former AFGC facility for isolation of RNA. Conclusion:ADD3 is the first mutant from our collection of temperature sensitive mutations affecting shoot, floral and root organogenesis to be studied at the transcriptome level.Our work modeling the evolution of gene duplicates and genetic redundancy suggests that temperature conditional redundancy may be common in plants (Pickett and Meeks-Wagner Plant Cell 19957 1347-1356)(Force,Lynch,Pickett et al. Genetics 1999151 1531-1545).A highly similar gene to the ADD3 candidate gene has been identified.An exploration of the utility of transcriptomics to describe phenotypic impacts of potential conditionally redundant mutants is particularly timely. Many reverse genetics experiments in Arabidopsis result in "mutants" displaying small or no impacts on phenotype.The completion of the Arabidopsis genome sequence suggests that this experience may become common.
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Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File
Pickett_1-1_ADD3_Rep1_ATH1191Col-3 gl1hypocotyls; cotyledons;meristems; true leaves 1 and 2; true leaves primordial initals Pickett_1-1_ADD3_Rep1_ATH1.cel
Pickett_1-2_ADD3_Rep2_ATH1193Col-3 gl1hypocotyls; cotyledons;meristems; true leaves 1 and 2; true leaves primordial initals Pickett_1-2_ADD3_Rep2_ATH1.cel
Pickett_1-3_wild-type_Rep1_ATH1190wild-typehypocotyls; cotyledons;meristems; true leaves 1 and 2; true leaves primordial initals Pickett_1-3_wild-type_Rep1_ATH1.cel
Pickett_1-4_wild-type_Rep2_ATH1192wild-typehypocotyls; cotyledons;meristems; true leaves 1 and 2; true leaves primordial initals Pickett_1-4_wild-type_Rep2_ATH1.cel