Seawater metagenome
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Project description:Saltwater aquarium tank mesocosm vertebrate 12S ribosomal locus
| PRJNA225954 | ENA
Project description:ADDOMEx Tier 3 Experiments: Mesocosm #1 and #2
| PRJNA320765 | ENA
Project description:Specimens of L. elliptica were collected by scuba divers at a depth of 10-18m in January 2010 at Hangar Cove, Rothera Point, Adelaide Island, Antarctic Peninsula (67°34’07°S, 68°07’30°W). Animals were collected in two size classes: large animals (with lengths ranging around 60mm) and small animals (lengths ranging around 30mm), the sizes of which equated to average ages of 16 and 7 years respectively. These two groups were termed “old” and “young” respectively. The clams were maintained in a flow-through aquarium and allowed to acclimate to laboratory conditions for 2 weeks before experimentation. At the end of the acclimation period, 10 old and 10 young animals were transferred to a 60l jacketed tank with aerated sea water, connected to a thermocirculator. The sea water temperature was gradually raised from 0°C to +3°C over a 12 hour period. This temperature was then maintained for a further 12 hours, before sampling the animals. Siphon tissue samples were dissected and immediately snap frozen in liquid nitrogen and stored at -80°C. The sampling regime was repeated on 10 old and 10 young animals that had been maintained in the flow-through aquarium for the same time period (control animals) RNA was extracted from all samples using TriSure, according to manufacturer’s instructions. RNAs from siphon tissue from 5 animals from each group (old treated, young treated, old control and young control) were used in the array hybridization experiments. The array used was A-MEXP-1676. PCR amplified labelled cDNA targets were prepared from 1μg total RNA. 5 replicates were used.
2016-02-29 | E-MTAB-3284 | biostudies-arrayexpress
Project description:Specimens of L. elliptica were collected by scuba divers at a depth of 10-18m in January 2010 at Hangar Cove, Rothera Point, Adelaide Island, Antarctic Peninsula (67°34’07°S, 68°07’30°W). Animals were collected in two size classes: large animals (with lengths ranging around 60mm) and small animals (lengths ranging around 30mm), the sizes of which equated to average ages of 16 and 7 years respectively. These two groups were termed “old” and “young” respectively. The clams were maintained in a flow-through aquarium and allowed to acclimate to laboratory conditions for 2 weeks before experimentation. At the end of the acclimation period, 10 old and 10 young animals were transferred to a 60l jacketed tank with aerated sea water, connected to a thermocirculator. The sea water temperature was gradually raised from 0°C to +3°C over a 12 hour period. This temperature was then maintained for a further 12 hours, before sampling the animals. Gill tissue samples were dissected and immediately snap frozen in liquid nitrogen and stored at -80°C. The sampling regime was repeated on 10 old and 10 young animals that had been maintained in the flow-through aquarium for the same time period (control animals) RNA was extracted from all samples using TriSure, according to manufacturer’s instructions. RNAs from gill from 5 animals from each group (old treated, young treated, old control and young control) were used in the array hybridization experiments. The array used was A-MEXP-1676. PCR amplified labelled cDNA targets were prepared from 1μg total RNA. 5 replicates were used with 3 dye swaps.
2016-02-28 | E-MTAB-3280 | biostudies-arrayexpress
Project description:Specimens of L. elliptica were collected by scuba divers at a depth of 10-18m in January 2010 at Hangar Cove, Rothera Point, Adelaide Island, Antarctic Peninsula (67°34’07°S, 68°07’30°W). Animals were collected in two size classes: large animals (with lengths ranging around 60mm) and small animals (lengths ranging around 30mm), the sizes of which equated to average ages of 16 and 7 years respectively. These two groups were termed “old” and “young” respectively. The clams were maintained in a flow-through aquarium and allowed to acclimate to laboratory conditions for 2 weeks before experimentation. At the end of the acclimation period, 10 old and 10 young animals were transferred to a 60l jacketed tank with aerated sea water, connected to a thermocirculator. The sea water temperature was gradually raised from 0°C to +3°C over a 12 hour period. This temperature was then maintained for a further 12 hours, before sampling the animals. Foot tissue samples were dissected and immediately snap frozen in liquid nitrogen and stored at -80°C. The sampling regime was repeated on 10 old and 10 young animals that had been maintained in the flow-through aquarium for the same time period (control animals) RNA was extracted from all samples using TriSure, according to manufacturer’s instructions. RNAs from foot tissue from 5 animals from each group (old treated, young treated, old control and young control) were used in the array hybridization experiments. The array used was A-MEXP-1676. PCR amplified labelled cDNA targets were prepared from 1μg total RNA. 5 replicates were used with 2 dye swaps.
2016-02-29 | E-MTAB-3282 | biostudies-arrayexpress
Project description:Specimens of L. elliptica were collected by scuba divers at a depth of 10-18m in January 2010 at Hangar Cove, Rothera Point, Adelaide Island, Antarctic Peninsula (67°34’07°S, 68°07’30°W). Animals were collected in two size classes: large animals (with lengths ranging around 60mm) and small animals (lengths ranging around 30mm), the sizes of which equated to average ages of 16 and 7 years respectively. These two groups were termed “old” and “young” respectively. The clams were maintained in a flow-through aquarium and allowed to acclimate to laboratory conditions for 2 weeks before experimentation. At the end of the acclimation period, 10 old and 10 young animals were transferred to a 60l jacketed tank with aerated sea water, connected to a thermocirculator. The sea water temperature was gradually raised from 0°C to +3°C over a 12 hour period. This temperature was then maintained for a further 12 hours, before sampling the animals. Mantle tissue samples were dissected and immediately snap frozen in liquid nitrogen and stored at -80°C. The sampling regime was repeated on 10 old and 10 young animals that had been maintained in the flow-through aquarium for the same time period (control animals) RNA was extracted from all samples using TriSure, according to manufacturer’s instructions. RNAs from mantle tissue from 5 animals from each group (old treated, young treated, old control and young control) were used in the array hybridization experiments. The array used was A-MEXP-1676. PCR amplified labelled cDNA targets were prepared from 1μg total RNA. 5 replicates were used with 1 dye swap.
2016-02-29 | E-MTAB-3283 | biostudies-arrayexpress
Project description:The interaction of animals with microbes relies on the specific recognition of microbial-derived molecules by receptors of the immune system. Sponges (phylum Porifera), as sister group of the Eumetazoa, provide insights into conserved mechanisms for animal-microbe crosstalk, but empirical data is limited. Here we aimed to characterize the immune response of sponges upon microbial stimuli by RNA-Seq. Two sponges species from the Mediterranean Sea, Aplysina aerophoba and Dysidea avara, were challenged with microbial-associated molecular patterns (lipopolysaccharide and peptidoglycan) or sterile artificial seawater (control) in aquarium experiments. Sponge tissue samples were collected 1h, 3h, and 5h after treatment. The response of the sponges to the treatments was assessed by differential gene expression analysis of RNA-Seq data. For each species, we compared the transcriptomic profiles of the samples in MAMP treatment to control within each time point.
2018-11-26 | E-MTAB-6757 | biostudies-arrayexpress
Project description:Hybridization of one kidney of cortisol treated fish vs. one kidney of control fish. Kidneys were collected from untreated juvenile sea bream (n=4) and from fish, which received for 72h a coconut-oil implant containing 10mg/Kg (fish wet weight) (n=4) cortisol. Experiments were carried out at the University of the Algarve, Portugal in accordance with National legislation for the welfare of animals. Experiments were conducted in two 125 l cylindriconical tanks supplied with a continuous through-flow of oxygenated seawater at 20+1 °C using juvenile sea bream (25 g + 3 g) adapted for 1 week to the experimental conditions. One tank contained 8 untreated fish (control) and the other tank 8 cortisol treated fish and the end of experiments fish were removed form tanks, decapitated and the kidneys rapidly removed and place in RNAlater (Qiagen) at –20 °C. No mortality occurred in the control tank but 2 fish died in the cortisol treated tank. Keywords: other
2007-01-26 | GSE2064 | GEO
Project description:A mutualistic relationship between reef-building corals and endosymbiotic algae (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. If, and to what extent, differences in algal symbiont clade contents can exert effects on the coral host transcriptome is currently unknown. In this study, we monitored algal physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered coral fragments using a custom cDNA gene expression microarray. Combining these analyses with results from algal and host genotyping revealed a striking symbiont effect on both the acclimated coral host transcriptome and the magnitude of the thermal stress response. This is the first study that links coral host transcriptomic patterns to the clade content of their algal symbiont community. Our data provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-algal partnerships. Sample Collection and Tank Experiment. On July 31 2007, six replicate fragments (9.5 ± 3.5cm2) were collected using hammer and chisel from the upper sun-exposed surface of five different, healthy-looking Montastraea faveolata colonies near Puerto Morelos, Quintana Roo, México (20o52â28.77âN and 86o51â04.53âW). The fragments were transported to the institute within 1 h and divided evenly between two 50 L aquaria (i.e., 3 fragments from each colony were placed into each tank) that received a constant flow of seawater (0.6 L/min). Each aquarium was fit with a water pump connected to a spray-bar to provide constant water movement and aeration. Both aquaria were placed in a common pond with flowing water to buffer diurnal temperature fluctuations, and both aquaria were acclimated to the same shaded ambient light condition. All coral fragments were mounted on plasticene and kept at a depth of 7 cm. From 10 to 19 August 2007, both aquaria received an average water temperature of 27.9 ± 0.6oC (as recorded by HOBO Light/Temperature Data Loggers, Onset Corp.). Beginning on 11 August, dark-adapted maximum quantum yields for charge separation (Fv/Fm) were measured at dusk for all coral fragments using a DIVING-Pulse Amplitude Modulated (PAM) fluorometer (Walz, Germany). Photosynthetically active radiation (PAR) was measured at noon and averaged 318 ± 129 µmol m-2 s-1. From 20 to 21 August 2007, all coral fragments were brought inside during the passage of Hurricane Dean. On 22 August, the experiment was reconstituted, and acclimation continued on 23 August and lasted until 1 September. During this time, both aquaria received a mean water temperature of 28.5 ± 0.8oC, and mean PAR of 371 ± 169 µmol m-2 s-1. On the night of 1 September, control time point samples from five different colonies were collected from each tank (Figure 1), before one 200-Watt aquarium heater was turned on in the treatment aquarium. A second heater was turned on 3 days later. During the thermal stress experiment, the control aquarium received mean water temperature of 28.8 ± 1.2oC; the heated aquarium, 31.5 ± 1.1oC. During the thermal stress experiment, tanks received mean PAR of 420 ± 152 µmol m-2 s-1. On 11 September, and 19 October, one sample each from five different colonies was collected from each tank for the bleaching and recovery time point, respectively. Microarray Gene Expression Analysis of Coral Host Gene Expression. For the biologically replicated time series experiment, a pool of RNA from all control tank fragments was used as a reference RNA sample, against which each sample from the treatment tank was competitively hybridized. All control and heat-stressed samples were competitively hybridized against the reference RNA. Dye swaps were not performed, as any dye bias present is equal in all comparisons to the reference. Note: Samples VALUEs used for statistical analysis of differential expression. GSE15253_shini_cbr_matrix2_norm.txt used for hierarchical clustering.
2010-05-18 | E-GEOD-15253 | biostudies-arrayexpress
Project description:Brain transcriptome at 0h, 1h, 3h, 6h, 12h, 24h, 48h after hypoxia stress Large yellow croakers (body weight at 90-100 g) were purchased from the mariculture farm in Ningde, Fuzhou, China. The fish were maintained at 25 °C in aerated water tanks (dissolved oxygen concentration: 7.8±0.5 mg per liter) with a flow through seawater supply. After 7 days of acclimation, these fish were used for the following experiments. Hypoxic time-course experiments were conducted at 25 °C using published method 30, by bubbling nitrogen gas into an aquarium. The desired pO2 was controlled by using dissolved oxygen meter (, Canada). At the onset of the time course, the oxygen content of the tank was lowered from an aerated pO2 of 100% (7.8 mg per liter) down to 20% (1.6±0.2 mg per liter) over a 30-min period. At the 1-, 3-, 6-, 12-, 24-, and 48-h time points, fish were sampled and sequenced.
2015-04-17 | E-GEOD-57608 | biostudies-arrayexpress