Ontology highlight
ABSTRACT:
PROVIDER: PRJNA967682 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24445700_1.fastq.gz | Fastqsanger.gz | |||
| SRR24445700_2.fastq.gz | Fastqsanger.gz | |||
| SRR24445701_1.fastq.gz | Fastqsanger.gz | |||
| SRR24445701_2.fastq.gz | Fastqsanger.gz | |||
| SRR24445702_1.fastq.gz | Fastqsanger.gz |
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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:To investigate a Florida manatee (Trichechus manatus latirostris) mortality event following a red tide bloom in Southwest Florida, a RNA-Seq experiment was conducted. Cell processes such as immune response, cell proliferation and differentiation and apoptosis were among the most affected by red tide. These were involved in potential diseases such as neoplasms, inflammation, and wounds and injuries, among others. There were both up-regulated and down-regulated genes, but the highest fold changes relative to controls were for genes that were down-regulated. Piccolo presynaptic cytomatrix protein (PCLO) gene, the one most down-regulated (fold change -9.93; p-value 0.0009) is associated with neurotransmitter release, cognitive functioning, neuronal loss, and neuronal synapse function. Another gene that has a similar function, ankyrin 2, neuronal, transcript variant 1 (ANK2) was also down-regulated (fold change -8.66; p-value 0.0023). ANK2 is associated with the stability of neuron synapses. Two immune genes, interleukin 6 (interferon, beta 2) (IL6) and zinc finger protein 804B (ZNF804B), were down-regulated (fold change -9.31; p-value 0.000003 and fold change -8.90; p-value 0.0164, respectively). Interleukin 6 encodes proteins involved in acute phase response, inflammation, and autoimmune response. ZNF804B is associated with neuronal chemokine and cytokine regulation, autoimmune response, and immune activation. The family with sequence similarity 186, member A (FAM186A) gene was down-regulated (fold change -8.79; p-value 0.0143). FAM186A gene mutation is associated with tumor metastasis in colorectal cancer tumors. Among the most up-regulated genes, CCAAT/enhancer binding protein (C/EBP) is involved in granulocytic differentiation and also involved with the immune system. Determining the differentially expressed genes associated with red tide enhances our understanding of manatee immune response to red tide toxins and aids in the development of red tide biomarkers. This information will better assist clinicians and researchers in diagnosing and treating future illnesses.
2017-10-01 | GSE86792 | GEO
Project description:The variability of the marine intertidal environment poses unique challenges for sessile species. Diurnal, tidal, and seasonal cycles introduce drastic variations in temperature, salinity, availability of nutrients and water. The California ribbed mussel Mytilus californianus is a filter feeder that dominates a middle range of the intertidal of many wave-swept rocky shores. The bivalve attaches to the substrate by several byssal threads. This sessile lifestyle allows us to accurately document the thermal history of an individual. We have profiled gene expression in M. californianus during a natural tidal cycle using a cDNA microarray composed of genes from mussels exposed to various stressors. Over three days, mussels were sampled from two sites differing in emersion exposure and average temperature. At each time point, three mussels were cut open in the field and frozen immediately on dry ice and stored at -80 degrees C until the gill, hepatopancreas, and adductor muscle were excised and processed for RNA extraction, reverse transcription, and hybridization to our microarrays. The resulting expression profile showed that genes involved in the cell cycle were diurnally regulated, heat shock proteins increased with temperature, and expression of several hundred other genes varied across the tidal cycle. Tide series (times and tide height): 26th July, low tide 0052, 0.8 ft; high tide 0705, 3.1 ft; low tide 1113, 2.4 ft; high tide 1810, 5.9ft. 27th July, low tide 0154, 0.1 ft; high tide 0837, 3.3 ft; low tide 1216, 2.7ft; high tide 1903, 6.2 ft. 28th July, low tide 0249, -0.6ft; high tide 0943, 3.5 ft; low tide 1323, 2.8ft; high tide 1903, 6.2ft. 15th Aug, low tide 0530, 0.26 ft; high tide 1200, 4.08 ft, low tide 0432, 2.65 ft; high tide 1036, 5.84 ft.
2007-07-30 | E-TABM-287 | biostudies-arrayexpress
Project description:In 2013, two large-scale Florida manatee (Trichechus manatus latirostris) mortality episodes were reported on separate coasts of Florida. The east coast mortality episode was associated with an unknown etiology in the Indian River Lagoon (IRL). The west coast mortality episode was attributed to a persistent Karenia brevis algal bloom or ‘red tide’ centered in Southwest Florida. To investigate these two mortality episodes, proteomic experiments using two-dimensional difference gel electrophoresis (2D-DIGE) followed by protein identification using liquid chromatography-tandem mass spectrometry (LC-MS/MS) were conducted, along with a separate gel-free analysis using isobaric tags for relative and absolute quantification (iTRAQ) LC-MS/MS. In comparison to the control group, manatees from the IRL, an area associated with an unknown mortality episode, displayed increased levels of several proteins in their serum samples. These increased proteins, which were identified in the iTRAQ experiment, included kininogen-1 isoform 1 (average ratio 1.38), protein AMBP (1.38), histidine-rich glycoprotein (1.34), properdin (1.30), and complement C4-A isoform 1 (1.25). In the red tide group, ceruloplasmin (2.32), pyruvate kinase isozymes M1/M2 isoform 3 (2.29), angiotensinogen (2.08), complement C4-A isoform 1 (1.83), and complement C3 (1.42) were increased. The proteins kininogen-1 isoform 1, histidine-rich glycoprotein, complement C4-A isoform 1, angiotensinogen, and complement C3 were also identified in increased levels in the 2D-DIGE experiment (Table 2b). These proteins are associated with acute-phase response, amyloid formation and accumulation, copper and iron homeostasis, the complement cascade pathway, and other important cellular functions. The increased level of complement C4 protein observed in both the red tide and unknown mortality episode groups was confirmed through the use of Western Blot.
2021-08-30 | PXD002470 | Pride
Project description:To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild. To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild.
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Project description:To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild. To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild. The expanded genome proxy array was designed as in (Rich et al., 2008). Briefly, each genotype was targeted using suites of ~20 70-mer oligonucleotide probes designed using the program ArrayOligoSelector (Zhu et al., 2003). Probes had approximately the same %GC (40%) and were distributed across the target genome or genome fragment, with no more than one probe per gene and avoiding 16S and 23S rRNA genes. The array included positive and negative control probes designed using the same method, to Halobacterium salinarum NRC-1 and a random genome sequence, respectively. The expanded array had a broader scope than the prototype of Rich et al., 2008 (268 target genotypes, as opposed to the prototype’s 14) and included a co-spot oligo for spot alignment and gridding purposes (using the “alien” oligo sequence of (Urisman et al., 2005). The targets were selected from fully-sequenced marine microbial genomes, publicly-available marine-derived BAC and fosmid clone sequences, and fully-sequenced clones from the lab’s Monterey Bay and Hawaii environmental BAC- and fosmid-based genomic libraries. Targeted genotypes are detailed in Table S1, summarized in Table S2, and presented in a schematic phylogenetic overview in Fig. 1. Previously-unpublished sequences used for array design were submitted to Genbank under accession numbers GU474833-GU474949. This submission presents the analysis of 57 samples, each hybridized to >= 3 arrays. In addition to negative control probes, for each hyrbdization date and run a negative control array was hyrbdized for which the input DNA was TE, taken through the entire aplification, labeling, and hybridization process.
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