Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1106198 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28850776_1.fastq.gz | Fastqsanger.gz | |||
| SRR28850776_2.fastq.gz | Fastqsanger.gz | |||
| SRR28850777_1.fastq.gz | Fastqsanger.gz | |||
| SRR28850777_2.fastq.gz | Fastqsanger.gz | |||
| SRR28850778_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Background: Crocus sativus L. belongs to the Iridaceae family and its dried stigma, called saffron, is one of the world’s most expensive spice. C. sativus is also a famous medicinal plant on account of producing significant pharmaceutical apocarotenoids like crocins, crocetin, picrocrocin and safranal. These metabolites have been reported to play important pharmacological efficiency towards many diseases. However, the regulatory mechanism of saffron apocarotenoids biosynthesis and stigma specific accumulation remains poorly understood. Results: In this work, we performed deep transcriptomic sequencing and dynamic metabolomic profiling of different developmental stage stigmas, and firstly integrated the dynamic changes of apocarotenoids with dynamic transcriptomic data. As a result, a co-expression network was constructed, and 41 pathway genes, 5 TF genes were identified as hub genes probably participating in apocarotenoid biosynthesis, validated by qRT-PCR. The reliability of these results was validated by previous research of several genes, which were also screened out by the co-expression network. Conclusions: This work provides novel insights into the mechanism by which the apocarotenoids is synthesized and regulated. Such gene-to-apocarotenoid landscapes associated with different developmental stigma are fundamental of deeply understanding the biosynthesis and metabolic engineering of saffron apocarotenoids in the C. sativus and other plant.
2019-12-09 | GSE103181 | GEO
Project description:Aim: To identify the genes and non-coding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary anti-oxidant (saffron) and of photobiomodulation. Methods: We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12h 5 lux, 12h darkness) are challenged by 24h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1mg/kg/day for 21d) or photobiomodulation (10 J/cm2 at the eye, daily for 5d). RNA from 1 eye of each of 4 animals in each of the 6 experimental groups (control, light damage (LD), saffron, photobiomodulation (PBM), saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate microarray results. Results: LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (P < 0.05 in comparisons with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes; by contrast, ncRNAs where prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62% respectively). Conclusions: Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given prior to retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for more focused study of their mechanisms. The were 3 biological repliactes of each of the following groups: Control, Saffron pretreated, Photobiomodulation pretreated, Light Damage, Saffron Light Damage and Photobiomodulation Light Damage. 18 chips in total were performed.
2010-07-16 | E-GEOD-22818 | biostudies-arrayexpress
Project description:In many plant species, flower stigma secretions are important in early stages of sexual reproduction. Previous chemical analysis and proteomic characterization of these exudates provided insights into their biological function. Nevertheless, the presence of nucleic acids in the stigma exudates has not been previously reported. Here we studied the stigma exudates of Pyrus communis, Pyrus pyrifolia and Pyrus syriaca, and showed them to harbor extracellular RNAs of various sizes. RNA sequencing revealed, for the first time, the presence of known Rosaceae mature micro-RNAs (miRs), also abundant in the stigma source tissue. Predicted targets of the exudate miRs in the Arabidopsis thaliana genome include genes involved in various biological processes. Several of these genes are pollen transcribed, suggesting possible involvement of exudate miRs in transcriptional regulation of the pollen. Moreover, extracellular miRs can potentially act across kingdoms and target genes of stigma interacting organisms/microorganisms, thus opening novel applicative avenues in HortSciences.
2023-11-15 | GSE225720 | GEO
Project description:Aim: To identify the genes and non-coding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary anti-oxidant (saffron) and of photobiomodulation. Methods: We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12h 5 lux, 12h darkness) are challenged by 24h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1mg/kg/day for 21d) or photobiomodulation (10 J/cm2 at the eye, daily for 5d). RNA from 1 eye of each of 4 animals in each of the 6 experimental groups (control, light damage (LD), saffron, photobiomodulation (PBM), saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate microarray results. Results: LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (P < 0.05 in comparisons with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes; by contrast, ncRNAs where prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62% respectively). Conclusions: Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given prior to retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for more focused study of their mechanisms.
2010-07-16 | GSE22818 | GEO
Project description:This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analysed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the Crocus genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions’ alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualise sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.
2021-03-24 | GSE166350 | GEO
Project description:RNA-Seq of Torenia fournieri: stigma and style
| PRJNA1084233 | ENA
Project description:RNA-seq of Brassicaceae pollen and stigma samples
| PRJNA600205 | ENA
Project 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. Keywords: rice (Oryza sativa L.), pollination and fertilization, stigma, molecular functions, signaling£¬microarray, stress response
2007-06-30 | GSE7951 | GEO
Project description:With nearly 140 α-glycosidases in 14 different families, plants are well equipped with enzymes that can break the α-glucosidic bonds in a large diversity of molecules. Here, we introduce activity profiling of α-glycosidases in plants using α-configured cyclophellitol aziridine probes carrying various fluorophores or biotin. In Arabidopsis, these probes label members of the GH31 family of Glycosyl Hydrolases, including ER-resident α-glucosidase-II RSW3/PSL5 and Golgi-resident α-mannosidase-II HGL1, which both trim N-glycans on glycoproteins. We also detect the active state of extracellular α-glycosidases such as α-xylosidase XYL1, which acts on xyloglucan in the cell wall to promote cell expansion, and α-glucosidase AGLU1, which acts in starch hydrolysis and can suppress fungal invasion. α-glycosidase labelling causes specific signals at 100-130 kDa that are pH-dependent and can be supressed by α-glycosidase inhibitors miglitol and acarbose. The α-glycosidase probes display similar miglitol-sensitive signals in leaf extracts of in a broad range of plant species. To show its use on a non-model plant, we applied glycosidase activity profiling on Crocus sativa, a cash crop for the production of saffron spice. Using a combination of biotinylated glycosidase probes, we identified and quantified 70 active glycosidases in stigma stages 1 and 4 of saffron (Crocus sativa L.), ten of which are differentially active. We also uncover massive changes in hydrolase activities in corms upon infection with Fusarium oxysporum using multiplex fluorescent labelling in combination with probes for serine hydrolases and cysteine proteases. These experiments demonstrate the ease by which active α-glycosidases and other hydrolases can be displayed in non-model plants.
2018-05-17 | PXD009014 | Pride