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 glyoxylate cycle knock-out mutants in early stages of seedling development
Description:We aim to assess changes in gene expression in the early stages of seedling growth in glyoxylate cycle enzyme knock-outs. The analysis has two clear goals: firstly to discover those genes (and hence enzymes) whose expression changes markedly when a major switch in the pathway of seed lipid mobilisation is imposed, and secondly to use information from metabolome analysis in the same mutants, to discover the impact of well-defined changes in endogenous metabolites on the transcriptome.In wild type seedlings at approximately 2 days post-imbibiton, glyoxylate cycle activity reaches a peak associated with the mobilisation of lipid reserves for the growth of the developing seedling. We have isolated KOs in two enzymes unique to the glyoxylate cycle: malate synthase (ms) and isocitrate lyase (icl). The mutants have a visible seedling phenotype only in the absence of sugar and/or (high) light. Surprisingly, these mutants are able to mobilise their lipid reserves, apparently via a switch from glyoxylate cycle and gluconeogenesis to respiration (Eastmond et al. 2000, PNAS 97: 5669-5674). Transcriptomic analysis will allow us to establish what changes take place in expression of key genes involved in respiration and gluconeogenesis when the glyoxylate cycle is blocked in the KOs. This will in turn provide insights into the pathways of metabolism operating in these plants.In addition we are already in the process of having these mutants analysed by the GARNet metabolomics facility to quantitate changes in organic acids, amino acids and sugars. The use of the transcriptomics facility in parallel will allow us to determine how specific changes in metabolite levels affect the expression of genes involved in carbon and nitrogen metabolism, as well as in seedling development as a whole. One major strength of our approach is that both ms and icl mutants are blocked in the glyoxylate cycle and so will result in many common changes to the metabolome, but each may produce novel changes in specific metabolites which might allow correlation with specific changes in the transcriptome. The joint analysis of metabolome and transcriptome data will be carried out in collaboration with members of our School of Informatics.Whole seedlings will be grown in vitro and harvested 2 days after transfer of imbibed seed to continuous light, and used for RNA extraction. This corresponds to Principle Growth Stage 0.7 in the convention of Boyes et al. (Plant Cell 13; 1499-1510, 2001). Each mutant has a specific wild type control (Columbia in one case and Ws in the other) giving four RNA samples in total.
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Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File
Cornah_1-10_A2-irv_Rep3_ATH1373col-0whole seedlings Cornah_1-10_A2-irv_Rep3_ATH1.cel
Cornah_1-11_A3-msx_Rep3_ATH1374WSwhole seedlings Cornah_1-11_A3-msx_Rep3_ATH1.cel
Cornah_1-12_A4-wsx_Rep3_ATH1375whole seedlings N5390Cornah_1-12_A4-wsx_Rep3_ATH1.cel
Cornah_1-13_msc_Rep1_ATH1701col-0whole seedlings N560987Cornah_1-13_msc_Rep1_ATH1.cel
Cornah_1-14_msc_Rep2_ATH1702col-0whole seedlings N560987Cornah_1-14_msc_Rep2_ATH1.cel
Cornah_1-15_msc_Rep3_ATH1703col-0whole seedlings N560987Cornah_1-15_msc_Rep3_ATH1.cel
Cornah_1-16_wtc_Rep1_ATH1704whole seedlings Cornah_1-16_wtc_Rep1_ATH1.cel
Cornah_1-17_wtc_Rep2_ATH1705whole seedlings Cornah_1-17_wtc_Rep2_ATH1.cel
Cornah_1-18_wtc_Rep3_ATH1706whole seedlings JC002_ATH1_A2.3-cornah-wtC.CEL
Cornah_1-1_A1-icl_Rep1_ATH1349col-0whole seedlings JC001_ATH1_A1-1-cornah-icl.CEL
Cornah_1-2_A2-irvl_Rep1_ATH1350col-0whole seedlings JC001_ATH1_A2.1-cornah-irv.CEL
Cornah_1-3_A3-msx_Rep1_ATH1351WSwhole seedlings JC001_ATH1_A3.1-cornah-msx.CEL
Cornah_1-4_A4-wsx_Rep1_ATH1352whole seedlings N5390JC001_ATH1_A4.1-cornah-wsx.CEL
Cornah_1-5_A1-icl_Rep2_ATH1368col-0whole seedlings JC001_ATH1_A1-2-cornah-icl.CEL
Cornah_1-6_A2-irv_Rep2_ATH1369col-0whole seedlings JC001_ATH1_A2.2-cornah-irv.CEL
Cornah_1-7_A3-msx_Rep2_ATH1370WSwhole seedlings JC001_ATH1_A3.2-cornah-msx.CEL
Cornah_1-8_A4-wsx_Rep2_ATH1371whole seedlings N5390JC001_ATH1_A4.2-cornah-wsx.CEL
Cornah_1-9_A1-icl_Rep3_ATH1372col-0whole seedlings JC001_ATH1_A1-3-cornah-icl.CEL