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GSE31077
Oryza sativa
16 Downloadable Samples
Affymetrix Rice Genome Array (rice)
Description
As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized.
Publication Title
Genome-wide analysis of the complex transcriptional networks of rice developing seeds.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Oryza sativa
- 10 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Expression profiles of protein coding genes were characterized using Affymetrix rice genome array to compare with expression profiles of miRNAs.
Publication Title
Characterization and expression profiles of miRNAs in rice seeds.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Light and brassinosteroids (BRs) have been proved to be crucial in regulating plant growth and development, however, the mechanism of how they synergistically function is still largely unknown. To explore the underlying mechanisms in photomorphogenesis, genome-wide analyses were carried out through examining the gene expressions of the dark-grown WT or BR biosynthesis-defective mutant det2 seedlings in presence of light stimuli, or exogenous Brassinolide (BL). Results showed that BR deficiency stimulates, while BL treatment suppresses, the expressions of light responsive genes and photomorphogenesis, revealing the negative effects of BR in photomorphogenesis. This is consistent with that genes involved in cell wall modification and cellular metabolism were specifically modulated by BL during dark-light transition, and altered expressions of genes related to energy utilization. Further analysis revealed that hormone biosynthesis and signaling related genes, especially those of auxin, were altered under BL treatment or light stimuli, indicating that BR may modulate photomorphogenesis through synergetic regulation with other hormones. Additionally, suppressed ubiquitin-cycle pathway during light-dark transition hinted the presence of a complicated network among light, hormone and protein degradation. The study provides the direct evidence of BR effects in photomorphogenesis and identified the genes involved in BR and light signaling pathway, which will help to elucidate the molecular mechanism of plant photomorphogenesis.
Publication Title
Genome-wide analysis revealed the complex regulatory network of brassinosteroid effects in photomorphogenesis.
Sample Metadata Fields
Age, Treatment
View Samples- Oryza sativa
- 4 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Expression profiles of seedling roots of rice mutant Osabl1 and wild-type under ABA treatment
Publication Title
Rice ABI5-Like1 regulates abscisic acid and auxin responses by affecting the expression of ABRE-containing genes.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Sel1L is an adaptor protein for the E3 ligase Hrd1 in the endoplasmic reticulum-associated degradation (ERAD), but its physiological role in a cell-type-specific manner remains unclear. Here we show that mice with adipocyte-specific Sel1L deficiency are resistant to diet-induced obesity and exhibit postprandial hypertriglyceridemia. Mechanistically, our data demonstrate a critical requirement of Sel1L for the secretion of lipoprotein lipase (LPL), independently of its role in Hrd1-mediated ERAD and ER homeostasis. Further biochemical analyses revealed that Sel1L physically interacts and stabilizes the LPL maturation complex consisted of LPL and lipase-maturation factor 1 (LMF1). In the absence of Sel1L, LPL is retained in the ER and prone to the formation of protein aggregates, which are degraded by autophagy-mediated degradation. The Sel1L-mediated control of LPL secretion is seen in other LPL-expressing cell types as well such as cardiac muscle and macrophages. Thus, our study reports a novel role of Sel1L in LPL secretion and systemic lipid metabolism.
Publication Title
The ER-associated degradation adaptor protein Sel1L regulates LPL secretion and lipid metabolism.
Sample Metadata Fields
Sex, Specimen part
View Samples- Oryza sativa
- 14 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
The receptor-like kinases (RLKs) plays critical roles in signal transduction through sensing the extracellular signals and activating the downstream signal transduction by phosphorylating their targets. Up to now, there are only a few RLKs have been functionally identified.
Publication Title
Global analysis of expression profiles of rice receptor-like kinase genes.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 29 Downloadable Samples
Ion Torrent Proton
Description
Psoriasis is a chronic inflammatory skin disease related to immune, whose complexity of molecular mechanisms is still not fully clear. RNA sequencing has been widely applied in various fields including biological medicine. According to the bioinformatics analysis of differential genes, biomarkers and drug targets have been discovered for the diagnosis and treatment of diseases. Besides, the pathological mechanisms of disease and functions of gene can be evaluated. In the present study, we report the application of RNA sequencing in skin tissues from psoriatic and healthy persons. By obtaining 2139 differential expressed genes (DEGs), 208 significantly differential GO terms and 44 significantly differential pathways were generated. We found that the functions of DEGs were mainly related to cell cycle, inflammatory, virus, immune response and metabolic process.The major pathways included cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, chemokine signaling pathway, cell cycle, metabolic pathways, ribosome, peroxisome, steroid biosynthesis and biosynthesis of unsaturated fatty acids. Furthermore, co-expression network was constructed to identify core genes and relations between genes. we considered genes with high values of degree and k-core difference in the co-expression network as core genes, such as IFNG, IL26, TLR3, PRKCQ, TLR4, CD274, CDK1 and IL17A. We chose CD274, an important immune checkpoint, to evaluate its regulatory mechanisms. Candidate genes related to CD274 were evaluated by the co-expression network analysis, and the relations between CD274 and candidate genes were validated in epidermal keratinocytes. Finally, IFNG and CDK1 inhibitor (indirubin) were found increasing the expression levels of CD274. In addition, indirubin was confirmed to attenuate mouse psoriasis-like skin lesion with the mechanisms related to CD274. In conclusion, this study provides us a comprehensive transcriptome analysis method on psoriasis to identify core genes and explore the important regulatory functions of genes. Overall design: Nine normal skins from healthy volunteers and 18 lesional skins from patients with psoriasis vulgaris were obtained for RNA sequencing
Publication Title
Indirubin attenuates mouse psoriasis-like skin lesion in a CD274-dependent manner: an achievement of RNA sequencing.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Oryza sativa
- 26 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Identification of factors regulating leaf inclination reveal a complex regulatory network of lamina joint development, however, the dynamic transcriptional programming of it remain to be elucidated.
Publication Title
Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 13 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
In angiosperms, stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. However, little is known about genes that regulate these processes in rice. Here we generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array. In total, we identified 665 probe sets (550 genes) to be expressed specifically or predominantly in the stigma papillar cells of rice. Real-Time quantitative RT-PCR analysis of 34 selected genes confirmed their stigma-specific expression. The expression of five selected genes was further validated by RNA in situ hybridization. Gene annotation shows that several auxin-signaling components, transporters and stress-related genes are significantly overrepresented in the rice stigma gene set. We also found that genes involved in cell wall metabolism and cellular communication appear to be conserved in the stigma between rice and Arabidopsis. Our results indicate that the stigmas appear to have conserved and novel molecular functions between rice and Arabidopsis.
Publication Title
Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Although a wide range of interactions between BRs and auxin have been recognized, knowledge about the direct molecular mechanism of interaction between them in specific physiological processes is very limited. In this study we found that auxin resisitent mutant msg2/iaa19 and arf7 were also resisitant to the BR effect on morphogenensis of dark-grown Arabidosis seedlings. Moreover, BR signaling transcription factor BZR1 can directly bind to promoter regions of IAA19 and ARF7.
Publication Title
Brassinosteroids regulate the differential growth of Arabidopsis hypocotyls through auxin signaling components IAA19 and ARF7.
Sample Metadata Fields
Specimen part, Treatment
View Samples