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GSE58603
Oryza sativa
35 Downloadable Samples
Affymetrix Rice Genome Array (rice)
Description
Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance.
Publication Title
Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Zea mays
- 23 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize.
Publication Title
Genome-wide transcriptome analysis of two maize inbred lines under drought stress.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 11 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola
Publication Title
Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 6 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
A near-isogenic rice line CSSL50-1 with high chalkiness and Asominori (the parental line) with normal grain endosperm were used for comparative studies of rice grain endosperm chalkiness,transcriptome comparison of 15 DAF caryopses using Affymetrix rice GeneChip identified differential expressed genes between these two lines.
Publication Title
Transcriptome analysis of grain-filling caryopses reveals involvement of multiple regulatory pathways in chalky grain formation in rice.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Oryza sativa
- 6 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes.
Publication Title
Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice.
Sample Metadata Fields
Specimen part
View Samples- Escherichia coli
- 6 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. coli exposed to 200 mM glyphosate.
Publication Title
Genome-wide transcriptional responses of Escherichia coli to glyphosate, a potent inhibitor of the shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase.
Sample Metadata Fields
Treatment
View Samples- Escherichia coli
- 6 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
A1501 aroA is a gene derived from Pseudomonas stutzeri A1501, encoding a class II glyphosate-tolerant EPSP synthase. To understand the effect of class II EPSP synthase to E. coli under glyphosate shock, we constructed the class II EPSP synthase-expressing plasmid pUC-A1501. And pUC18 is the empty vector used as a control.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 6 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
In order to elucidate the molecular mechanism of gibberellin (GA)-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying GA promotion of maize mesocotyl elongation. These studies showed that the GA receptor GID1, the transcriptional factor MYB, and the genes encoding DELLA protein DWRF8, kinases, Raf, LRR, RLCK, and involved in flavonoid biosynthesis, aminosugars metabolism, cell wall synthesis and modification, might play critical roles in maize mesocotyl elongation.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 6 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
In order to elucidate the molecular mechanism of auxin-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying IAA promotion of maize mesocotyl elongation. Under deep-sowing condition, IAA is transported by auxin transporter-like protein 1 and binds to auxin binding protein ABP20, which results in degradation of Aux/IAA and de-repressing of auxin-inducible genes. Then, transcriptional factor such as MYB, kinase such as LRR, fructose and mannose metabolism and so on are activated. Finally, genes involved in cell wall synthesis and modification are expressed so that mesocotyl elongation of 3681-4 is promoted. Furthermore, gene expression of a key enzyme ACO in ethylene biosynthesis and ethylene receptor ETR2 were up-regulated after the treatment with 10-4 M IAA, which suggested that mesocotyl elongation of 3681-4 inclined to be inhibited when the concentration of applied IAA was increased from 10-4 M to 10-3 M.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway.
Sample Metadata Fields
Specimen part
View Samples