E-MEXP-2267
Ontology highlight
ABSTRACT:
PROVIDER: E-MEXP-2267 | ExpressionAtlas | 2015-11-27
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MEXP-2267-analysis-methods.tsv | Tabular | |||
| E-MEXP-2267-atlasExperimentSummary.Rdata | Rdata | |||
| E-MEXP-2267-configuration.xml | Xml | |||
| E-MEXP-2267-percentile-ranks.tsv | Tabular | |||
| E-MEXP-2267.condensed-sdrf.tsv | Tabular |
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Project description:RNAseq profiling of seeds and 7 time points during germination in rice under aerobic and anerobic conditions, as well as following re-oxygenation.
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Project description:To investigate global changes in gene expression during B. emersonii germination process, we constructed cDNA microarrays containing 3,563 putative unique genes. Analyses were carried out during germination induced under various environmental conditions. Microarray data revealed that 26% of them are differentially expressed during germination in nutrient medium, in at least one of the time points investigated. Over 500 genes are up regulated during the time course of germination under these conditions, most of them being related to cell growth, including genes involved in protein biosynthesis, DNA transcription, energetic metabolism, carbohydrate and oligopeptide transport, and cell cycle control. On the other hand, several transcripts stored in the zoospores are down regulated during germination in nutrient medium, such as genes involved in signal transduction, amino acid transport and chromosome organization. We also compared germination induced in the presence of nutrients with that triggered either by adenine or potassium ions in inorganic salt solution. Several genes involved in cell growth that are induced during germination in nutrient medium do not show increased expression when B. emersonii zoospores germinate in inorganic solution, indicating that nutrients exert a positive regulatory effect on the transcription of these genes.
2009-01-05 | GSE12883 | GEO
Project description:affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30M-BM-0C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in M-bM-^@M-^\EM-bM-^@M-^] while the endosperm samples are abbreviated M-bM-^@M-^\AM-bM-^@M-^]. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition). 36 arrays - rice; organ comparison,time course
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Project description:To investigate global changes in gene expression during B. emersonii germination process, we constructed cDNA microarrays containing 3,563 putative unique genes. Analyses were carried out during germination induced under various environmental conditions. Microarray data revealed that 26% of them are differentially expressed during germination in nutrient medium, in at least one of the time points investigated. Over 500 genes are up regulated during the time course of germination under these conditions, most of them being related to cell growth, including genes involved in protein biosynthesis, DNA transcription, energetic metabolism, carbohydrate and oligopeptide transport, and cell cycle control. On the other hand, several transcripts stored in the zoospores are down regulated during germination in nutrient medium, such as genes involved in signal transduction, amino acid transport and chromosome organization. We also compared germination induced in the presence of nutrients with that triggered either by adenine or potassium ions in inorganic salt solution. Several genes involved in cell growth that are induced during germination in nutrient medium do not show increased expression when B. emersonii zoospores germinate in inorganic solution, indicating that nutrients exert a positive regulatory effect on the transcription of these genes. Differentially expressed genes during germination were investigated in a time-course experiment, using RNA samples isolated from cells collected 30, 60 and 90 min after inoculation of zoospores in nutrient medium DM3. The reference sample was zoospore RNA, which was considered the time zero of germination. We also compared germination in nutrient medium with germination induced in inorganic salt solution, triggered either by adenine or potassium ions. In these experiments we considered germination in nutrient medium as the reference sample. There are at least 3 biological replicates (independent harvest) and 2 technical replicates for each array (L-left and R-right).
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Project description:Transcript abundance profiles were examined over the first 24 hours of germination in rice grown under anaerobic conditions. Transcript abundance profiles were also examined for rice grown under aerobic conditions for 24 h and then switched to anaerobic conditions and vice versa.
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Project description:Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.
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Project description:affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30°C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in “E” while the endosperm samples are abbreviated “A”. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition).
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