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Browse MaizePLEX Experiment Data

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Profiling expression changes caused by a segmental aneuploid in maize
Nathan,M,Springer, University of Minnesota, Saint Paul, Minnesota (springer@umn.edu)
Experiment design (8 hybridizations)
genetic line
•wildtype •aneuploid(DpDf)

This experiment has been imported by PLEXdb from NCBI GEO (GSE10243)

Series_summary:
ABSTRACT: BACKGROUND: While changes in chromosom...[complete overview]

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Experiment Name: Profiling expression changes caused by a segmental aneuploid in maize
Accession No: ZM23
Microarray: maize18k
Visibility: public
Experiment Type:
Experiment Factor(s):
genetic line
•wildtype   •aneuploid(DpDf)
Quality Control: biological replicates
Treatment summary:
 genetic line  # replicates
 wildtype  4
 aneuploid(DpDf)  4
Total hybridizations: 8
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE10243)

Series_summary:
ABSTRACT: BACKGROUND: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated. RESULTS: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that ~40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage. CONCLUSIONS: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions.

Keywords: Genotype comparison of wild-type and segmental aneuploid

Series_overall_design:
There are four biological replicates of pooled wild-type siblings and four biological replicates of pooled DpDf plants. The DpDf plants are segmental aneuploids that contain three copies of the short arm of chromosome 5. These plants are all in the B73 inbred genetic background.
Publication: 'Profiling expression changes caused by a segmental aneuploid in maize.', Makarevitch I, Phillips RL, Springer NM
BMC Genomics 2008 Jan 10;9:7.
pubmed: 18186930
Created: 2009-04-30 13:06:21
Last Update: 2009-04-30 13:29:27
GEO Accession GSE10243
Submitter: PLEXdb Curator
Name: Nathan,M,Springer
Institution: University of Minnesota, Saint Paul, Minnesota
Head of Laboratory: --
email(s):
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