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:Ecotype specific nitrogen responses in the Arabidopsis root
Description:OVERVIEWRoot branching in response to changes in nitrogen status in the soil is a dramatic example of the plant's remarkable developmental plasticity. To characterise natural variation in root architectural plasticity at the molecular level we compared root nitrogen responses across a panel of seven ecotypes.AIMIn recent work we investigated the genetic architecture of developmental plasticity in the root at the phenotypic, genetic, and transcriptional levels by combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in seven ecotypes. This series contains the microarray expression data for seven ecotypes that represent a range of root branching strategies. The microarrays detailed the global programme of gene and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.EXPERIMENTAL SETUPThe nitrogen response in seven Arabidopsis thaliana ecotype (Col0, Kas2, NFA8, SQ8, TAMM27, Ts5, Var2-1) whole roots was assayed using microarrays. Seedlings were grown hydroponically in basal MS containing no nitrogen except 0.5mM ammonium succinate and 3mM sucrose for 12 days in long day conditions in a Percival. At dawn on day twelve, 5mM KNO3 (nitrogen treatment) or 5mM (control) was added to the hydroponic medium for 2 hours. At the end of the treatment time roots were harvested and flash-frozen in liquid nitrogen for subsequent RNA extraction. Total RNA was extracted using Trizol, then standard Affymetrix protocols were used to label RNA and hybridise to the Affymetrix ATH1 Array which was stained using the 'EukGE-WS2v4_450' protocol and scanned using the Affymetrix GeneChip 3000 Scanner. The whole experiment was carried out in triplicate with 42 chips in total (14 experiments).
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Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File