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Series GSE21480 Query DataSets for GSE21480
Status Public on May 19, 2011
Title Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of perennial woody plants, poplar.
Platform organism Populus sp.
Sample organism Populus trichocarpa
Experiment type Expression profiling by array
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.
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.
Contributor(s) Ko J, Han K
Citation(s) 21383024
Submission date Apr 22, 2010
Last update date Jan 02, 2015
Contact name Jae-Heung Ko
Phone 82-31-201-3863
Organization name Kyung Hee University
Department Plant & Environmental Resources
Street address 1 Seocheon-dong, Giheung-gu
City Yongin
State/province Gyeonggi
ZIP/Postal code 446-701
Country South Korea
Platforms (1)
GPL4359 [Poplar] Affymetrix Poplar Genome Array
Samples (4)
GSM537035 Pt_summer_1
GSM537036 Pt_summer_2
GSM537037 Pt_winter_1
BioProject PRJNA126037

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE21480_RAW.tar 23.3 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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