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| Status |
Public on Oct 23, 2011 |
| Title |
Microarray data from pre-germinated seeds and hypoxia-treated seedlings of Arabidopsis prt6-1 and ate1 ate2 mutants of the N-end rule pathway of targeted proteolysis pathway |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
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| Summary |
This study analyzes transcriptome profiles in pre-germinated seeds and hypoxia-treated seedlings of Arabidopsis thaliana wild type (Col-0) and homozygous mutants (prt6-1 and ate1 ate2). This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls. For pre-germinated seeds, seeds imbibed for 24 h were used for total RNA extraction. For hypoxia treatment, 7-d-old seedlings were incubated in a hypoxia chamber for 2 h and the entire seedling was subjected to RNA extraction. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome during early seed germination stage and in response to hypoxia in seedlings were evaluated. The data led to identification of mRNAs with abundance regulated by PRT6 and ATE1 / ATE2, which are essential components for the N-end rule pathway of targeted proteolysis (NERP). A combination of genetic, biochemical and molecular analyses reveal that NERP coordinates the stability of key ethylene responsive factor (ERF) family transcription factors, which regulate expression of core hypoxia response genes and tolerance to low oxygen stress. This indicates that the NERP functions as a homeostatic sensor of low oxygen in plants.
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| Overall design |
Pre-germinated seeds; 2 genotypes (Col-0 and prt6-1) x 3 independent biological replicate experiments: Hypoxia treated seedlings; 3 genotypes (Col-0, prt6-1, and ate1 ate2) x 2 treatments (2h aerobic and 2h hypoxia) x 2 independent biological replicate experiments.
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| Contributor(s) |
Lee SC, Isa NM, Holdsworth M, Bailey-Serres J |
| Citation(s) |
22020279, 24462115 |
| Submission date |
Jun 13, 2011 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Takeshi Fukao |
| E-mail(s) |
fukao@ucr.edu
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| Organization name |
University of California, Riverside
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| Street address |
Department of Botany and Plant Sciences
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| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
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| Platforms (1) |
| GPL198 |
[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array |
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| Samples (18)
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| GSM741155 |
Pre-germinated seeds, prt6-1, rep 1 |
| GSM741156 |
Pre-germinated seeds, prt6-1, rep 2 |
| GSM741157 |
Pre-germinated seeds, prt6-1, rep 3 |
| GSM741158 |
Aerobic-seedlings, Col-0, rep 1 |
| GSM741159 |
Aerobic-seedlings, Col-0, rep 2 |
| GSM741160 |
Aerobic-seedlings, prt6-1, rep 1 |
| GSM741161 |
Aerobic-seedlings, prt6-1, rep 2 |
| GSM741162 |
Aerobic-seedlings, ate1 ate2, rep 1 |
| GSM741163 |
Aerobic-seedlings, ate1 ate2, rep 2 |
| GSM741164 |
Hypoxic-seedlings, Col-0, rep 1 |
| GSM741165 |
Hypoxic-seedlings, Col-0, rep 2 |
| GSM741166 |
Hypoxic-seedlings, prt6-1, rep 1 |
| GSM741167 |
Hypoxic-seedlings, prt6-1, rep 2 |
| GSM741168 |
Hypoxic-seedlings, ate1 ate 2, rep 1 |
| GSM741169 |
Hypoxic-seedlings, ate1 ate 2, rep 2 |
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| Relations |
| Affiliated with |
GSE69995 |
| BioProject |
PRJNA140775 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE29941_RAW.tar |
35.4 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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