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:Global Transcript Profiling of the Green Sectors of the immutans Variegation mutant of Arabidopsis
Description:Green and white variegation in the Arabidopsis immutans (im) mutant is caused by a nuclear recessive gene. The green sectors contain cells with normal-appearing chloroplasts, while cells in the white sectors have photooxidized plastids lacking organized lamellae. The white and green cells of im have the same genotype (im im), i.e., the tissues are not genetic chiamaeras of wild-type and mutant tissue. The green im sectors have altered leaf morphology, higher than normal rates of carbon assimilation (monitored by 14CO2 uptake) and corresponding increases in the activities of Rubisco and SPS, elevated starch and sucrose pool sizes, and an altered pattern of carbohydrate partitioning that favors sucrose over starch. To gain insight into the morphological and biochemical changes observed in the immutans green sectors, we conducted microarray studies to ask whether or not the immutans green sectors and wild-type Arabidopsis leaves had similar transcriptomes. For these experiments, we used the Affymetrix oligorrays (~22,500 genes) and compared the population of RNAs from dissected green sectors of mature im leaves to the population of RNAs from similarly-aged Columbia leaves growing under the same continuous light (100 µmoles m-2 s-1) conditions. Total RNA was isolated using the TRIzol Reagent (GIBCO BRL, Rockville, MD) according to the manufacturers protocol. RNA samples were prepared from wild-type Arabidopsis leaves and im green leaf sectors randomly collected from multiple 3-4 wk old plants; three independent collections were performed and six microarray slides (3 replicates) were used to analyze mRNA abundances in each sample. cDNAs were prepared from 10 µg of total RNA following instructions in the Affymetrix GeneChip Expression Analysis manual, and the double-stranded cDNAs were biotinylated by in vitro transcription using the BioArray High Yield RNA Transcript Labeling Kit (ENZO Diagnostics Inc. Farmingdale, NY). The labeled probe (cRNA) was then purified using an RNeasy column (Qiagen. Valencia, CA). Approximately 20 µg of fragmented (940C for 25 min) cRNA was sent to the University of Iowa DNA Facility for hybridization, staining and scanning of the Affymetrix Arabidopsis oligoarrays. Signal intensities and detection calls were generated by Affymetrix Microarray Suite v5.0 software (Affymetrix Inc., Santa Clara, CA) and exported to Microsoft EXCEL. The data were then loaded into GeneSpringR v5.1 for detailed statistical analysis.
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Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File
Aluru_1-1_WT1_Rep1_ATH140253-4 wk old fully expanded leaves Aluru_1-1_WT1_Rep1_ATH1.CEL
Aluru_1-2_WT2_Rep2_ATH140263-4 wk old fully expanded leaves Aluru_1-2_WT2_Rep2_ATH1.CEL
Aluru_1-3_WT3_Rep3_ATH140273-4 wk old fully expanded leaves Aluru_1-3_WT3_Rep3_ATH1.CEL
Aluru_1-4_imG1_Rep1_ATH140283-4 wk old fully expanded leaves N3218Aluru_1-4_imG1_Rep1_ATH1.CEL
Aluru_1-5_imG2_Rep2_ATH140293-4 wk old fully expanded leaves N3218Aluru_1-5_imG2_Rep2_ATH1.CEL
Aluru_1-6_imG3_Rep3_ATH140303-4 wk old fully expanded leaves N3218Aluru_1-6_imG3_Rep3_ATH1.CEL