Freshwater stream A-B-E amplicon
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB37542 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Stream biofilms from four Swiss streams Metagenome
| PRJNA414706 | ENA
Project description:Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic planktonic bacteria, dwelling in freshwater systems (lakes, ponds, and streams) across all climatic zones and across all continents. This includes habitats characterised by strongly fluctuating environmental conditions. So the experiments were designed to mimick winter and summer scenarios with additional impact of UV irradiation. Comparative transcriptomic studies were conducted to analyse gene-expression levels in contrasting experimental conditions. Overall, molecular candidates were revealed that may contribute in rapid acclimatisation of this strain in their immediate environment.
2017-10-31 | GSE98129 | GEO
Project description:The goal of this study was to use global gene expression as a diagnostic tool to compare hepatic gene expression patterns in both male and female FHM in streams with the lowest and highest reproductive success, and potentially identify a suite of mRNA transcripts indicative of reproduction in a population The goal of this study was to compare differences in hepatic mRNA expression between gender at high and low egg-producing streams, not differences between individual streams. A k-means cluster analysis was performed using eggs/pair/day on the original 17 streams to delineate 3 clusters: high, medium and low. From that analysis, FHM from 6 of the original 17-streams used in Crago et al. (2010) were chosen for the microarray experiment (Fig. 1, Table 1). In this study the experimental condition is reproductive success; High versus Low reproductive success. The streams grouped into High Reproductive Success were Oak Creek-2007 (2313 eggs), Point Creek (1277 eggs), Meeme Creek (1164 eggs) and Baird Creek (967 eggs). The streams grouped into Low Reproductive Success were: Ashwaubenon Creek (0 eggs), Devils Creek (541 eggs) and Oak Creek-2006 (642 eggs). Multiple regression analysis using the 22 sediment and water quality characteristics measured in the 6 streams with the highest (n = 4 and lowest (n = 3) streams demonstrated that there were no differences amongst the streams in regards to measure sediment and water variables. .5 One array was run for each gender from each stream. So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth. There were 14 arrays used in this study, 7 for males, 7 for females from individual rivers. So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth. In the case of Oak Creek, which was sampled in both years, there was a large difference in egg production between two years. Therefore separate arrays were run for Oak Creek 2006 and Oak Creek 2007. All streams chosen had overall survival rates of at least 80% through the 21-day sampling period, except Devils River. The survival rate for Devils River was at 100% until four days prior to the end of the experiment when six fish died or escaped.
2014-04-09 | E-GEOD-56604 | biostudies-arrayexpress
Project description:The three life domains microbial communities of a tropical soda lake
| PRJEB24947 | ENA
Project description:C2C12 myoblasts were infected with a retrovirus expressing Pax7d or with an empty virus (puro) as a control. All of the samples originated from the same common pool of parental C2C12. This pool was split into six streams. A single prep of Pax7d-puro virus was split into three volumes and used to infect three of the streams. A single prep of puro-alone virus was similarly split in three and used to infect the remaining three streams. From the point of the infection forward each stream was maintained distinct from the others. Cells were infected and grown simultaneously under identical conditions. The puro samples may be reused as controls for future experiments, and therefore were immediately hybridized to the MOE430A and MOE430B chips in order to generate a complete dataset. The Pax7d samples, as a specific component of this experiment, were only hybridized to the MOE430A chip as a first-look into the system. Experiment Overall Design: this experiment include 2 samples and 9 replicates
2008-06-12 | E-GEOD-3224 | biostudies-arrayexpress
Project description:C2C12 myoblasts were infected with a retrovirus expressing Pax7d or with an empty virus (puro) as a control. All of the samples originated from the same common pool of parental C2C12. This pool was split into six streams. A single prep of Pax7d-puro virus was split into three volumes and used to infect three of the streams. A single prep of puro-alone virus was similarly split in three and used to infect the remaining three streams. From the point of the infection forward each stream was maintained distinct from the others. Cells were infected and grown simultaneously under identical conditions. The puro samples may be reused as controls for future experiments, and therefore were immediately hybridized to the MOE430A and MOE430B chips in order to generate a complete dataset. The Pax7d samples, as a specific component of this experiment, were only hybridized to the MOE430A chip as a first-look into the system. Keywords: other
2005-09-01 | GSE3224 | GEO
Project description:Streams Impacted By Hydraulic Fracturing Activity--Microcosms with Biocides
| PRJNA476929 | ENA
Project description:The sea-run phenotype of rainbow trout (Oncorhynchus mykiss), like other anadromous salmonids, present a juvenile stage fully adapted to life in freshwater known as parr. Development in freshwater is followed by the smolt stage, where preadaptations needed for seawater life are developed making fish ready to migrate to the ocean, after which event they become post-smolts. While these three life stages have been studied using a variety of approaches, proteomics has never been used for such purpose. The present study characterised the blood plasma proteome of parr, smolt and post-smolt rainbow trout using a gel electrophoresis liquid chromatography tandem mass spectrometry approach alone or in combination with low-abundant protein enrichment technology (combinatorial peptide ligand library). In total, 1,822 proteins were quantified, 17.95% of them being detected only in plasma post enrichment. Across all life stages, the most abundant proteins were ankyrin-2, DNA primase large subunit, actin, serum albumin, apolipoproteins, hemoglobin subunits, hemopexin-like proteins and complement C3. When comparing the different life stages, 17 proteins involved in mechanisms to cope with hyperosmotic stress and retinal changes, as well as the downregulation of nonessential processes in smolts, were significantly different between parr and smolt samples. On the other hand, 11 proteins related to increased growth in post-smolts, and also related to coping with hyperosmotic stress and to retinal changes, were significantly different between smolt and post-smolt samples. Overall, this study presents a series of proteins with the potential to complement current seawater-readiness assessment tests in rainbow trout, which can be measured non-lethally in an easily accessible biofluid. Furthermore, this study represents a first in-depth characterisation of the rainbow trout blood plasma proteome, having considered three life stages of the fish and used both fractionation alone or in combination with enrichment methods to increase protein detection.
2020-01-07 | PXD016570 | Pride