Ontology highlight
ABSTRACT:
PROVIDER: PRJNA848830 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Post-fire soil bacteria (16S) and eukaryotes (18S) raw rRNA sequence reads from Mediterranean dry sclerophyll woodland and adjacent historically cleared and grazed pastures.
| PRJNA847045 | ENA
Project description:Neotyphodium coenophialum is an endophytic fungus that infects most tall fescue (Festuca arundinacea) pastures that are commonly used in animal grazing systems in the United States. Beef cattle grazing such pastures are impaired in health and production performance, resulting in a large economic loss in US food-animal production systems. Based on clinical and biochemical blood analyte profiles, hepatic targeted gene and protein analyses, and hepatic transcriptomic profiling, microarray analysis using the WT Btau 4.0 Array (version 1.0, Affymetrix, Inc., Santa Clara, CA) was conducted to determine if grazing endophyte-infected tall fescue pastures affects pituitary gene expression profiles of growing beef steers. The specific overall hypothesis tested was that grazing high endophyte-infected pasture would alter the pituitary genomic expression profiles of the same growing steers, especially genes involved in production and secretion of prolactin, growth hormone, thyroid stimulating hormone, and adrenocorticotropic hormone. Sixteen steers were assigned to graze either a low toxic endophyte tall fescue-mixed grass (LE treatment, 5.7 ha, n = 8) or a high toxic endophyte infected tall fescue (HE treatment, 5.7 ha, n = 8) pasture located in the University of Kentucky Agricultural Research Center. All steers had ad libitum access to fresh water, an industry standard mineral-vitamin supplement, and grazed respective pastures for 89 to 105 days. Whole pituitaries were collected for RNA extraction and microarray analysis.
2014-10-23 | E-GEOD-62570 | biostudies-arrayexpress
Project description:Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972). The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24–31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE™) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159 002 14-mer SAGE™ tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher®) and expressed sequence tag (EST) sequences. The analysis of 14 559 unique SAGE™ tags, which were present more than once in our SAGE™ library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE™ tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level. Keywords: paddock samples, pasture, perennial ryegrass, Serial Analysis of Gene Expression (SAGE™), season specific expression, monocot Ryegrass tissue Perennial ryegrass (Lolium perenne L.) cv. Bronsyn was used throughout this study. Field-grown samples, comprising mainly viable leaves and pseudostems, were collected at midday from livestock-active monocultural paddocks at Dexcel, Hamilton, New Zealand during the peak of each season, and frozen immediately in liquid nitrogen. Samples were transported in dry-ice and stored at ?80 oC until use. During spring and summer, care was taken not to include any floral stems in the tissue sample. Grass samples were collected from pregrazed (15–60 days post-grazing) and post-grazed (1 day post-grazing) ryegrass swards, which were visibly healthy and free of any pests. Construction of SAGE™ libraries RNA was extracted using TRIZOL® reagent (Invitrogen, Carlsbad,CA, USA). For each SAGE™ library, 100 ug of pre- and post-grazed sample-derived total RNA was employed, and the libraries were created using an I-SAGE™ or I-SAGE™Long Kit (Invitrogen) according to the manufacturer’s protocol. Pre- and post-grazed SAGE™ libraries were sequenced at the Australian Genome Research Facility (Brisbane, Australia), and the tags were extracted using SAGE2000 software and combined to produce the transcript profile for the season.
2006-11-08 | E-GEOD-5211 | biostudies-arrayexpress
Project description:Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacleM-^Rs surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution.
2013-10-01 | E-MTAB-1902 | biostudies-arrayexpress
Project description:Small RNA sequencing was performed in woodland strawberry fruits for study of chromatin structure.
2024-09-25 | GSE208609 | GEO
Project description:This series represents Experiment 1 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration. Keywords = BY4743 Keywords = desiccation Keywords = glucose-limited Keywords = rehydration Keywords = yeast Keywords: time-course
2005-08-01 | GSE1311 | GEO
Project description:This series represents Experiment 3 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration. Keywords = BY4743 Keywords = desiccation Keywords = glucose-limited Keywords = rehydration Keywords = yeast Keywords: time-course
2005-08-01 | GSE1313 | GEO
Project description:This series represents Experiment 2 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration. Keywords = BY4743 Keywords = desiccation Keywords = glucose-limited Keywords = rehydration Keywords = yeast Keywords: time-course
2005-08-01 | GSE1312 | GEO
Project description:The dry season is a major challenge for Plasmodium falciparum parasites in many malaria endemic regions, where water availability limits mosquitoes to only part of the year. How P. falciparum bridges two transmission seasons months apart, without being cleared by the host or compromising host survival is poorly understood. Here we show that low levels of P. falciparum parasites persist in the blood of asymptomatic Malian individuals during the 5- to 6-month dry season, rarely causing symptoms and minimally affecting the host immune response. Parasites isolated during the dry season are transcriptionally distinct from those of subjects with febrile malaria in the transmission season, reflecting longer circulation within each replicative cycle, of parasitized erythrocytes without adhering to the vascular endothelium. Low parasite levels during the dry season are not due to impaired replication, but rather increased efficiency of splenic clearance of longer-circulating infected erythrocytes. We propose that P. falciparum virulence in areas of seasonal malaria transmission is regulated so that the parasite decreases its endothelial binding capacity, allowing increased splenic clearance and enabling several months of subclinical parasite persistence.
2020-08-20 | GSE148125 | GEO