Resource diversity and nutritional quality
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40121 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4556480_1.fastq.gz | Fastqsanger.gz | |||
| ERR4556480_2.fastq.gz | Fastqsanger.gz | |||
| ERR4556490_1.fastq.gz | Fastqsanger.gz | |||
| ERR4556490_2.fastq.gz | Fastqsanger.gz | |||
| ERR4556500_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 302 |
Similar Datasets
Project description:Purpose: Parts of Europe and the United States have witnessed dramatic losses in commercially managed honey bees over the past decade to what is considered an unsustainable extent. The large-scale loss of honey bees has considerable implications for the agricultural economy because honey bees are one of the leading pollinators of numerous crops. Honey bee declines have been associated with several interactive factors. Poor nutrition and viral infection are two environmental stressors that pose heightened dangers to honey bee health. Methods: We used RNA-sequencing to examine how monofloral diets (Rockrose and Chestnut) and Israeli acute paralysis virus inoculation influence gene expression patterns in honey bees. Results: We found a considerable nutritional response, with almost 2,000 transcripts changing with diet quality. The majority of these genes were over-represented for nutrient signaling (insulin resistance) and immune response (Notch signaling and JaK-STAT pathways). Somewhat unexpectedly, the transcriptomic response to viral infection was fairly limited. We only found 43 transcripts to be differentially expressed, some with known immune functions (argonaute-2), transcriptional regulation, and muscle contraction. We created contrasts to determine if any protective mechanisms of good diet were due to direct effects on immune function (resistance) or indirect effects on energy availability (tolerance). A similar number of resistance and tolerance candidate differentially expressed genes were found, suggesting both processes may play significant roles in dietary buffering from pathogen infection. We also compared the virus main effect in our study (polyandrous colonies) to that obtained in a previous study (single-drone colonies) and verified significant overlap in differential expression despite visualization methods showing differences in the noisiness levels between these two datasets. Conclusions: Through transcriptional contrasts and functional enrichment analysis, we add to evidence of feedbacks between diet and disease in honey bees. We also show that comparing results derived from polyandrous colonies (which are typically more natural) and single-drone colonies (which usually yield more signal) may allow researchers to identify transcriptomic patterns in honey bees that are concurrently less artificial and less noisy. Altogether, we hope this work underlines possible merits of using data visualization techniques and multiple datasets when interpreting RNA-sequencing studies.
2018-10-30 | GSE121885 | GEO
Project description:Nutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanism of nutritional programming. The live-bearing fish Xiphophorus multilineatus, has the potential to be a new model for understanding these mechanisms, given evidence of both genetic and nutritional programming influences on juvenile growth rate. To study the molecular signatures of nutritional programming, we assembled a de novo transcriptome for X. multilineatus, and used RNA-Seq to profile gene expression in the brains of males reared in low and high quality juvenile environments. We found131 genes were differentially expressed, including metabolism and appetite master regulator agrp gene.
2017-01-15 | GSE89561 | GEO
Project description:Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. We aim at understanding the genomic influence on milk quality and synthesis by comparing two sheep breeds, with different milking attitude, Sarda and Gentile di Puglia, using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we generated the first annotated microarray developed for sheep with a covering of most of the genome.
2009-11-30 | GSE18619 | GEO
Project description:The Global Diversity lines are a resource collection of 87 strains of Drosophila melanogaster (Grenier JK et al 2015. PMID 25673134). In this experiment, whole adult flies from the Global Diversity Lines (87 inbred lines derived from natural populations) were profiled using a spotted-oligo microarray to determine natural variation in gene expression patterns.
2016-03-17 | E-MTAB-4580 | biostudies-arrayexpress
Project description:Plant growth-promoting rhizobacteria (PGPR) are soil microbes that can promote plant growth and/or increase plant resistance to one or multiple stress conditions. These natural resources are environmentally friendly tools for reducing the use of chemical fertilizers and pesticides and for improving the nutritional quality of plants, including pharmacological metabolites. Coriander (Coriandrum sativumL.), commonly known as cilantro or Chinese parsley, is a worldwide culinary and medicinal plant with both nutritional and medicinal properties. Little is known about how PGPR may promote plant growth or affect metabolite profiles in coriander. Here, by usingAeromonassp. H1 that is a PGPR strain, we investigate how coriander yield and quality could be affected by PGPR with transcriptome insights.
2024-03-11 | GSE247080 | GEO
Project description:Human Developmental Biology Resource (HDBR) expression resource-RNAseq
| PRJEB14594 | ENA
Project description:Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. We aim at understanding the genomic influence on milk quality and synthesis by comparing two sheep breeds, with different milking attitude, Sarda and Gentile di Puglia, using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we generated the first annotated microarray developed for sheep with a covering of most of the genome. Whole tissue samples of mammary gland were collected from 4 lactating individuals of two sheep (Ovis aries) breeds, Gentile di Puglia and Sarda. Biopsies of lactating mammary tissue were taken at two lactation stages (first record, stage 01: 6 days after lambing; second record, stage 02: 44 days after lambing) in both breeds. Tissues from mammary gland were immersed in RNAlater (Sigma) immediately after biopsy and stored at -20°C.
2010-05-19 | E-GEOD-18619 | biostudies-arrayexpress
Project description:Microcystis cells under the nutritional stress conditions
2024-09-13 | PXD048427 |
Project description:The Human Developmental Biology Resource (HDBR) expression resource is a new resource for studying prenatal human brain development. It consists of two parts which have been uploaded as two submissions: HDBR expression resource- RNAseq (E-MTAB-4840, this submission) and HDBR expression resource- SNP data (E-MTAB-4843). It is unique in the age range (4 post conception weeks [PCW] to 17PCW) and number of brains studied, particularly those under 8PCW. It is also unique in that both the large-scale data sets and the corresponding RNA and DNA samples are available, the latter via the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR; http://www.hdbr.org). There are 628 RNA-seq datasets from different regions of the brains studied. The number of regions depends on the stage and size of the sample and/or the tissue available. Embryos (4-8PCW) have been staged using a modified Carnegie staging system, details can be found at http://database.hudsen.eu/. All the RNAseq datasets from the same brain have the same embryo/fetus number (e.g. RNAseq datasets HDBR251-HDBR254 are from different tissues from embryo number 1406). The embryo/fetus ID number is recorded in the individual column. The majority of the brains studied are between 4 and 12PCW. During this time the major brain regions are established and there are the early stages of cortex development. DNA was prepared from all the tissues used for RNA-seq analysis and SNP genotype data generated from one tissue from each brain. RNA-seq data and SNP-data from the same tissue and brain have the same name (e.g. HDBR469). There are also SNP genotype data from 229 additional specimens in paraffin wax blocks available for individual gene expression studies. These data are in the accompanying HDBR expression resource- SNP data (E-MTAB-4843).
2016-10-12 | E-MTAB-4840 | biostudies-arrayexpress
Project description:Xenopus tropicalis Mutation Resource
| PRJEB2073 | ENA