Ontology highlight
ABSTRACT:
PROVIDER: PRJNA694367 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Shotgun metagenomics of virion (0.22 micrometer filtrate) in Lake Biwa (2016-2017)
| PRJDB7309 | ENA
Project description:Varese Lake 2016-2017 bloom 16S V3-V4 amplicons
| PRJNA694444 | ENA
Project description:Shotgun metagenomics of bacterioplankton in Lake Biwa (2016)
| PRJDB6644 | ENA
Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to investigate spring microbial functional genes in mesocosm-simulated shallow lake ecosystems having been undergoing nutrient enrichment and warming for nine years.
2020-12-30 | GSE155582 | GEO
Project description:62 individual Brassica napus plants of the same accession grown in the same field were expression-profiled in autumn 2016 and phenotyped extensively until harvest in spring 2017. Machine learning models were used to link gene expression to the phenotypes of individual plants, with the purpose of assessing how much phenotype information in encoded in ‘noisy’ gene expression variation among individual plants of the same background grown under the same uncontrolled field conditions. Rosette leaf 8 blades of 62 individual Brassica napus plants of the same winter-type accession (BnASSYST-120, Darmor) grown in the same field (50°58'24.9\\"N 3°46'49.1\\"E, Merelbeke, Belgium) were RNA-seq profiled. No treatments or stresses were applied, all plants were profiled individually under uncontrolled field conditions. Sown at 2016-09-08, rosette leaf 8 sampled for RNA-seq at 2016-11-28, plants harvested at 2017-06-13.
2022-10-10 | E-MTAB-11904 | biostudies-arrayexpress
Project description:Bacteria isolated from a Lake Erie Microcystis bloom in 2017
| PRJNA521711 | ENA
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101
2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress
Project description:Transcranial direct current stimulation (tDCS) has been applied in experimental and clinical settings for more than twenty years and may facilitate rehabilitation after stroke as suggested by clinical data (Hummel et al. 2005, Sparing et al. 2009). Intriguingly, tDCS evokes various cellular effects exceeding its primary neurophysiological actions: We previously described subacute effects of tDCS on immune- and stem cells in the rat brain (Rueger et al. 2012, Keuters et al. 2015, Pikhovych et al. 2016, Braun et al. 2016). However, the effects of tDCS on immune-mediating genes have not yet been investigated. To investigate the more immediate effects of tDCS regulating those cellular responses, we treated rats with a single session of either anodal or cathodal tDCS, and analyzed the gene expression by microarray; sham-stimulated rats served as control. We confirmed the effects of gene upregulation by immunohistochemistry at the protein level. We here report for the first time that acute anodal transcranial direct current stimulation enhanced the expression of several genes coding for MHC-I, affecting inflammation and synaptic plasticity (Neumann et al. 1995, Shatz et al. 2009). Moreover, cathodal tDCS increased expression of the gene encoding for the immunoregulatory protein Osteopontin. Osteopontin has beneficial effects on neural stem cells and microglia after brain damage such as stroke (Rabenstein et al. 2015, Rabenstein et al. 2016, Ladwig et al. 2017, Rogall et al. 2017). Overall, our data indicate that a specific modulation of neuroinflammatory processes by non-invasive brain stimulation constitutes a promising therapeutic option with immediate translational relevance.
2019-10-31 | E-MTAB-8318 | biostudies-arrayexpress