Microorganism in Saffron
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA437542 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6824040_1.fastq.gz | Fastqsanger.gz | |||
| SRR6824040_2.fastq.gz | Fastqsanger.gz | |||
| SRR6824050_1.fastq.gz | Fastqsanger.gz | |||
| SRR6824050_2.fastq.gz | Fastqsanger.gz | |||
| SRR6824060_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 56 |
Similar Datasets
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: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:Crocus sativus isolate:Saffron JU | cultivar:Saffron Genome sequencing and assembly
| PRJNA734464 | ENA
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:soil from saffron rhizosphre Metagenome
| PRJNA978949 | ENA
Project description:Introduction: The high market value of saffron (Crocus sativus L.) has made it an attractive candidate for adulteration. Safflower (Carthamus tinctorius L.) and tartrazine are among the most common herbal and synthetic foreign materials that may be added to pure saffron for the purpose of adulteration. In spite of encouraging advances achieved in the identification of adulteration in saffron samples, the lack of a simple method with sufficient power for discrimination of pure high grade saffron from meticulously adulterated saffron samples persuaded us to perform this study. Objectives: In this work, we show that 1H NMR spectroscopy together with chemometric multivariate data analysis methods can be used for the detection of adulteration in saffron. Methods: Authentic Iranian saffron samples (n?=?20) and adulterated samples that were prepared by adding either different quantities of natural plant materials such as safflower, or synthetic dyes such as tartrazine or naphthol yellow to pure saffron (n?=?22) composed the training set. This training set was used to build multivariate Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) models. The predictive power of the PLS-DA model was validated by testing the model against an external dataset (n?=?13). Results: PCA and PLS-DA models could both discriminate between the authentic and adulterated samples, and the external validation showed 100% sensitivity and specificity for predicting the authenticity of suspicious samples. Peaks specific to authentic and adulterated samples were also characterized. Proximity of samples with unknown adulteration status to the samples adulterated with known compounds in the PCA provided insight regarding the identity of the adulterant in the suspicious samples. Furthermore, the authentic samples could be distinguished based on their cultivation site. Conclusion: The present study demonstrates that the application of 1H NMR spectroscopy coupled with multivariate data analysis is a suitable approach for detection of adulteration in saffron specimens. Outstanding sensitivity and specificity of the PLS-DA model in discriminating the authentic from adulterated samples in external validation confirmed the high predictive power of the model. The advantage of the present method is its power for detecting a wide spectrum of adulterants, ranging from synthetic dyes to herbal materials, in a single assay.
2017-07-20 | MTBLS331 | MetaboLights