Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1005600 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25642047_1.fastq.gz | Fastqsanger.gz | |||
| SRR25642047_2.fastq.gz | Fastqsanger.gz | |||
| SRR25642048_1.fastq.gz | Fastqsanger.gz | |||
| SRR25642048_2.fastq.gz | Fastqsanger.gz | |||
| SRR25642049_1.fastq.gz | Fastqsanger.gz |
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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:<p>Saffron (Crocus sativus) is a high-value crop prized in culinary and pharmaceutical applications for its nutritional and therapeutic properties. However, corm rot caused by Fusarium oxysporum severely compromises yield and quality. Here, we isolated F. oxysporum strain CSP01 from diseased corms and confirmed it as the primary causal agent. Five endophytic fungi-CS05 (Trametes versicolor), CS06 (Bjerkandera adusta), CS07 (Phlebia acerina), CS33 (Penicillium sp.), and CS65 (Trichoderma sp.)-were screened for biocontrol efficacy against CSP01. CS05 showed the strongest suppression, achieving a 75.97% control rate and outperforming the positive controls Mortierella alpina and Trichoderma harzianum. To elucidate CS05-mediated protection, we integrated transcriptomic, proteomic, and metabolomic analyses. Transcriptome profiling revealed robust induction of host defense genes following CS05 treatment, particularly in phenylpropanoid biosynthesis (PAL2, 4CL1, CCR4), jasmonic acid (JA) signaling (COI1), and hydrogen peroxide (H2O2) metabolism (CAT1). Metabolomic analysis identified 461 differentially accumulated metabolites in CS05-treated corms; notably, L-tyrosine, coniferin, and p-coumaraldehyde were enriched within phenylpropanoid pathways and associated with enhanced resistance. qRT-PCR and enzyme activity assays validated the involvement of PAL2, 4CL1, and CCR4 in phenylpropanoid biosynthesis. Phytohormone measurements showed significantly elevated JA in CS05-treated corms (12.774 pmol/L) relative to pathogen-only corms (7.773 pmol/L). Oxidative stress assessments indicated that H2O2 in infected corms peaked at day 30 (41.189 mmolg-1 protein); at day 24, infected corms contained 20.904 mmolg-1 protein versus 16.760 mmolg-1 protein in CS05-treated corms, demonstrating mitigation of excessive reactive oxygen species. Collectively, these results show that T. versicolor CS05 enhances saffron resistance to corm rot by coordinating phenylpropanoid pathway activation, amplifying JA signaling, and improving H2O2 detoxification. This study provides the first evidence that T. versicolor CS05 is an effective, eco-friendly biocontrol agent for saffron corm rot and offers mechanistic insight into endophyte-driven plant defense, supporting its potential for sustainable disease management.</p>
2026-06-01 | MTBLS14647 | MetaboLights
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:Analysis of WI-38 cells treated with Crocin I. Crocin I is a major active component of saffron. Results provide insight into protective effect of Crocin I against WI-38 cells senescence.
2026-06-23 | GSE335498 | 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:This project integrates Label-free quantification based proteomics with computational structural analyses to identify, quantify, and characterize key proteins involved in saffron apocarotenoid biosynthesis across different developmental stages of saffron plant. This integrative strategy is expected to generate a comprehensive understanding of stage-specific protein dynamics.
2026-06-01 | PXD076029 | Pride