Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1327264 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study aims to provide referrable transcriptomic data for the exploration of floral pigment biosynthesis in hyacinth cultivars. This dataset consists of 189 RNA-Seq libraries prepared for seven cultivars at different developmental stages and perianth partitions, generated 1256.8 gigabytes data in total. After removal of adaptor trimming and quality trimming, the qualified sequences were adopted for de novo assembly of mRNA. The gene expressions were quantified as read counts and then normalized into FPKM. This study provides the first profiling on the gene expression of hyacinth, contributing to the new-generation molecular breeding in producing noval hyacinth cultivars.
2025-01-12 | GSE286406 | GEO
Project description:Current protection strategies against the fungal pathogen Botrytis cinerea rely on a combination of conventional fungicides and host genetic resistance. Defence elicitors can stimulate plant defence mechanisms through a phenomenon known as priming. Priming results on a faster and/or stronger expression of resistance upon pathogen attack. This work aims to study priming of a commercial formulation of the elicitor Chitosan. Treatments with Chitosan result in induced resistance in solanaceous and brassicaceous plants. Large-scale transcriptomic analysis in this study revealed that Chitosan primes gene expression at early time-points after infection. Four conditions were analysed using microarrays: (i) water-treated and non-infected plants (Water + Mock); (ii) Chitosan-treated and non-infected plants (Chitosan + Mock); (iii) water-treated and B. cinerea-infected plants (Water + B. cinerea); (iv) Chitosan-treated and B. cinerea-infected plants (Chitosan + B. cinerea). Inoculations were performed four days after treatment with Chitosan, and leaf discs from four independent plants (biological replicates) per treatment were sampled at 6 h, 9 h and 12 h post-inoculation (hpi) with water mock or B. cinerea spores.
2020-07-01 | E-MTAB-8868 | biostudies-arrayexpress
Project description:Daphnia magna is a bio-indicator organism accepted by several international water quality regulatory agencies. Current approaches for assessment of water quality rely on acute and chronic toxicity that provide no insight into the cause of toxicity. Recently, molecular approaches, such as genome wide gene expression responses, are enabling an alternative mechanism based approach to toxicity assessment. While these genomic methods are providing important mechanistic insight into toxicity, statistically robust prediction systems that allow the identification of chemical contaminants from the molecular response to exposure are needed. Here we apply advanced machine learning approaches to develop predictive models of contaminant exposure using a D. magna gene expression dataset for 36 chemical exposures. We demonstrate here that we can discriminate between chemicals belonging to different chemical classes including endocrine disruptors, metals and industrial chemicals based on gene expression. We also show that predictive models based on indices of whole pathway transcriptional activity can achieve comparable results while facilitating biological interpretability.
2013-01-17 | GSE43564 | GEO
Project description:Dracunculus medinensis, also called the Guinea worm, is a nematode that causes dracunculiasis, a debilitating neglected tropical disease in humans. The parasite is currently targeted by the global Guinea Worm Eradication Program (GWEP). Historically, GWEP in endemic countries have focused on interrupting transmission of the disease through intervention such as isolation and management of patients, health education, provision of improved water sources and promotion of filtering drinking water from unimproved water sources to avoid ingestion of the copepod intermediate host (IH) that may contain infectious third-stage larvae, and treatment of water sources to kill copepods. The recent shift of Guinea worm infections in animals - particularly domestic dogs - has introduced an additional challenge to the eradication program, underscoring the urgent need for diagnostics and therapeutics. Understanding the parasite biology and survival strategies in the mammalian host, the copepod IH, and fresh water is pivotal to identifying new control measures. Comparative transcriptomic analysis provides a powerful tool to uncover the molecular mechanisms underlying parasite survival and adaptations. Here, we compared the transcriptome of adult gravid female and first-stage larvae (L1), the stage infective for the copepod IH. Comparative transcriptomic analysis of two adult females and their L1 revealed an upregulation of genes involved in translation, transcription, and DNA repair in L1, likely reflecting adaptations essential for survival in freshwater and subsequent infection of copepods. Additionally, genes involved in cuticle formation were upregulated in adult females highlighting the role of cuticle integrity in retaining millions of L1 until the gravid female worm emerges. We identified highly expressed genes in the adult female that may represent promising candidates for diagnostic markers.This study provides novel insights into the biology of the Guinea worm by examining the transcriptome of L1 and adult female stages. These findings could support the development of novel diagnostics and therapeutics to advance the ongoing eradication effort.
2025-07-19 | GSE302616 | GEO
Project description:Inflammation initiated in response to microbial encounter, or deliberately induced upon vaccination, is central for the activation of adaptive lymphocytes. The stimulation of pattern recognition receptors (PRRs) orchestrates the inflammatory programs that regulate adaptive immunity. Nevertheless, only few PRRs have been tested for their capacity to potentiate the efficacy of vaccines. Here, we took advantage of a mRNA-based vaccine generated against the ancestral Spike protein of SARS-CoV-2 to test whether tuning inflammation enhances the efficacy of the vaccine. We combined a mRNA-based vaccine with the mannadjuvant, a formulation of fungal mannan and alum hydroxide that targets a class of PRRs known as C-type lectin receptors. The mannadjuvant increased the magnitude and durability of the response elicited by the mRNA-based vaccine, and it also led to the induction of neutralizing antibodies directed against variants of concern with a high escape capacity. Overall, our data demonstrate that inflammation can be harnessed to create more potent and durable mRNA-based vaccines.
2025-10-09 | GSE255778 | GEO
Project description:Amplicon-based fungal metagenomic sequencing for the identification of fungal species in brain tissue from Alzheimer's disease. The study consists in 14 samples, sequenced using Illumina's paired-end technology.
| EGAD00001003196 | EGA
Project description:whole genome Oxford Nanopore sequencing and assembly: water hyacinth (Eichhornia crassipes)
| PRJNA704546 | ENA