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Series GSE16068 Query DataSets for GSE16068
Status Public on Jan 01, 2011
Title Functional genomic analysis of a nitrate reductase knockdown relative to wild-type in model-ecosystems (mesocosm)
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Current advances in genomics and computational biology have afforded novel insight as to how the phenotype is generated from the genotype – systems biology. We argue that systems biology, when viewed through an ecological lens, provides an unprecedented opportunity to understand how genes cascade through multiple levels of biological organization to alter ecosystem function. To test this approach, we established six monocultures of Arabidopsis thaliana ‘Columbia’- wild-type plants, six monocultures of a single gene variant (mutant) to the wild-type, and six mixtures with equal density plantings of each genotype in mesocosm chambers (50 x 50 x 45 cm). The mutant harbored a T-DNA insertion in the main nitrate reductase gene (nia2). This is the gateway enzyme for N metabolism, which resulted in activity levels that were 38% of the wild-type. Mesocosms were instrumented to monitor soil and air temperature, water and humidity status, and CO2 differentials. Transcript expression profiles were generated for each of the monoculture populations by collecting and processing 100 leaves per mesocosm at generation 2 and 4.
 
Overall design Design: Expression profiles were generated for each monoculture population by pooling 100 leaves per mesocosm into one sample. This resulted in 6 biological replicates for each genotype per generation. Thus, a total of 48 samples were generated (6 wild-type + 6 nia2 mutants x 2 generations x 2 CO2 treatments) and hybridized onto microarrays. We used a direct loop design analyzing generations separately (diagrams of hybridization designs are linked as supplementary PDF files).
 
Contributor(s) Weston DJ, Stan WD
Citation(s) 26306170
Submission date May 12, 2009
Last update date Apr 06, 2020
Contact name David J Weston
E-mail(s) westondj@ornl.gov
Phone 865 241-8323
Fax 865 576-9939
Organization name David Weston
Department Environmental Sciences Division
Street address Bldg. 1062 Rm. 210
City Oak Ridge
State/province TN
ZIP/Postal code 37830
Country USA
 
Platforms (1)
GPL7092 Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATq306.01.Z)
Samples (24)
GSM402157 Nia_elev_gen2_1_vs_Nia_amb_gen2_1
GSM402158 nia_amb_gen2_2_vs_nia_elev_gen2_2
GSM402159 Wt_amb_gen2_1_vs_nia_amb_gen2_3
Relations
BioProject PRJNA115491

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE16068_Design_generation_2.pdf.gz 46.5 Kb (ftp)(http) PDF
GSE16068_Design_generation_4.pdf.gz 45.3 Kb (ftp)(http) PDF
GSE16068_Normalized_intensity_values.xls.gz 12.6 Mb (ftp)(http) XLS
GSE16068_RAW.tar 70.7 Mb (http)(custom) TAR (of GPR)
Processed data are available on Series record

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