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Browse PoplarPLEX Experiment Data

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Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of perennial woody plants, poplar.
Jae-Heung Ko, Kyung Hee University, Department of Plant & Environmental Resources, Yongin, South Korea (ko@msu.edu)
Experiment design (4 hybridizations)
growth condition
•summer •winter

This experiment has been imported by PLEXdb from NCBI GEO (GSE21480)

Series_summary:
Winter survival and maintenance strategy is cruc...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of perennial woody plants, poplar.
Accession No: PT30
Microarray: Poplar61k
Visibility: public
Experiment Type:
Experiment Factor(s):
growth condition
•summer   •winter
Quality Control: biological replicates
Treatment summary:
 growth condition  # replicates
 summer  2
 winter  2
Total hybridizations: 4
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE21480)

Series_summary:
Winter survival and maintenance strategy is crucial in temperate woody plants. Here, we demonstrate novel aspects of the transcriptional regulations adopted by perennial tree species in winter/dormancy, employing a biochemical and whole transcriptome analysis. As expected, genes related to cold hardiness and defense are over-represented. Interestingly, carbohydrate biosynthesis and transport-related genes were very actively expressed in winter/dormancy. Further biochemical analyses verified the dormancy/winter transcription phenotype. Furthermore, dormancy/winter preferential expression of genes involved in the cell wall biosynthesis/modification, circadian rhythm, the indirect transcriptional regulation (RNA metabolism), and chromatin modification/remodeling were identified. Taken together, regulation of gene expression in the winter survival and maintenance may include not only controlled by promoter binding transcription factors but may also be regulated at the post-transcriptional and chromatin levels.

Series_overall_design:
In the first step towards the understanding of molecular mechanisms underlying the winter survival and maintenance of perennial trees, we examined the characteristics of transcription phenotype of the dormancy/winter stem compared to the active growth/summer stem by using a whole transcriptome analysis (GeneChip Poplar Genome Array; Affymetrix). Poplar Genome Array has a total of 61,251 probe sets, representing 57,423 poplar gene models, and allows us to interrogate a total of 41,558 unique gene models because of the probe set redundancy. Slight redundancy of the probe sets within a single chip gave us a unique opportunity to have internal comparisons of the particular genes. Very high reproducibility (R2 > 0.97) between the replicated samples was found. Further confirmation of the GeneChip data was made by semi-quantitative RT-PCR analysis using several genes showing the summer or winter biased expression. Based on these results, further analysis of winter stem transcriptome against summer stem was performed.
Publication: 'Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of poplar.', Ko JH, Prassinos C, Keathley D, Han KH.
Tree Physiol 2011 Feb;31(2):208-25.
pubmed: 21383024
Created: 2011-07-29 10:05:17
Last Update: 2011-07-29 12:06:37
Released: 2011-07-29
GEO Accession GSE21480
Submitter: PLEXdb Curator
Name: Jae-Heung Ko
Institution: Kyung Hee University, Department of Plant & Environmental Resources, Yongin, South Korea
Head of Laboratory: Kyung-Hwan Han
email(s):
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