http://lod.bco-dmo.org/id/dataset/881469 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2022-09-27 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Genetic accessions, treatment information, and methodology from laboratory experiments studying transcriptomic responses to saxitoxin in zebrafish (Danio rerio) 2022-09-27 publication 2022-09-27 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2022-09-28 publication https://doi.org/10.26008/1912/bco-dmo.881469.1 Neelakanteswar Aluru Woods Hole Oceanographic Institution principalInvestigator Mark Hahn Woods Hole Oceanographic Institution principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Aluru, N., Hahn, M. (2022) Genetic accessions, treatment information, and methodology from laboratory experiments studying transcriptomic responses to saxitoxin in zebrafish (Danio rerio). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-09-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.881469.1 [access date] Dataset Description: &lt;p&gt;The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible through GEO Series accession number GSE204989 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE204989).&lt;br /&gt; &lt;br /&gt; Sequence Read Archive (SRA) data, BioSamples, and GEO holdings can be accessed from the NCBI BioProject PRJNA843039 (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA843039).&lt;/p&gt; Methods and Sampling: &lt;p&gt;Adult zebrafish (Tupfel-Long fin wild type strain) were raised under ambient conditions (temperature 28.5 degrees, photoperiod 10:14 light/dark) in Redfield zebrafish facility. Embryos used in the experiment were obtained by tank breeding of the adults. Embryos were injected with saxitoxin or vehicle control at 6 hours post-fertilization.&lt;br /&gt; &lt;br /&gt; Zebrafish embryos were exposed to saxitoxin (STX; 24 or 48 pg) or vehicle (0.3 mM HCl) at 6 hours post fertilization (hpf) via microinjection. We examined transcriptional profiles in embryos at 24, 36 and 48 hpf using RNA sequencing.&lt;br /&gt; &lt;br /&gt; &lt;strong&gt;Sampling and analytical procedures:&lt;/strong&gt;&lt;br /&gt; Total RNA was isolated from embryos at 3 developmental time points and RNAseq was carried out using Illumina platform.&lt;br /&gt; &lt;br /&gt; &lt;strong&gt;Organism scientific name:&lt;/strong&gt; Danio rerio&lt;br /&gt; LSID (Life Sciences Identifier) = urn:lsid:marinespecies.org:taxname:1026595&lt;br /&gt; NCBI:txid903980&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1314642 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1314642 Funding provided by National Institutes of Health (NIH) Award Number: NIH-P01ES021923 Award URL: https://reporter.nih.gov/project-details/8388954#details completed Neelakanteswar Aluru Woods Hole Oceanographic Institution naluru@whoi.edu pointOfContact Mark Hahn Woods Hole Oceanographic Institution 266 Woods Hole Road Woods Hole MA 02543 USA mhahn@whoi.edu pointOfContact asNeeded Dataset Version: 1 Unknown Illumina HiSeq 2000 theme None, User defined Automated DNA Sequencer instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Woods Hole Center for Oceans and Human Health https://www2.whoi.edu/site/whcohh/ Woods Hole Center for Oceans and Human Health NSF Award Abstract The mission of the Woods Hole Center for Oceans and Human Health is to protect the public health through enhanced understanding of how oceanic and environmental processes including climatic variation affect the population dynamics of toxin producing organisms, and the risks from exposure to their potent neurotoxins. Factors affecting the distribution, survival, proliferation, and toxicity of harmful algal bloom (HAB) species still are poorly known, despite their enormous consequences for human health. Three research projects and two cores comprise the Center. The Center structure will facilitate the integration among projects, and the integration of research with education and community engagement activities. The Center will engage stakeholders, facilitate education on HAB science at many academic levels, and strengthen public knowledge about HAB blooms and their impacts. The Center is jointly supported by NSF and by the National Institute for Environmental Health Sciences (NIEHS). The research activities of the Center will focus on two key HAB taxa: Alexandrium fundyense that produces the saxitoxins responsible for paralytic shellfish poisoning (PSP), and Pseudo-nitzschia spp. that produce domoic acid responsible for the amnesic shellfish poisoning (ASP) syndrome. Novel, targeted, efficient, and data-rich sampling approaches developed by the applicants and applied in situ have revealed that critical aspects of A. fundyense dynamics in natural settings differ dramatically from those inferred from laboratory studies, indicating plasticity in response to climate. The research proposed will build on these new and fundamental insights into what regulates blooms, and on the Center's established strengths in ocean observation technologies and modeling, to predict how environmental variables may influence population dynamics of known and emerging HAB threats. Hindcast simulations compared with climate data records in the Gulf of Maine will assess model performance and uncertainty. Forecasts run for a range of potential climate scenarios can help quantify future public health risks. Similarly, specific cells have been identified in the developing brain that are targets of HAB toxins, findings giving insights into developmental toxicological mechanisms. These will guide studies to address the scope of toxin effect in the developing central nervous system, potentially linking developmental exposures to adult consequences. Studies of new mechanisms of toxin action will include determination of the effects of combined or repeated exposure to sub-lethal levels of saxitoxin and domoic acid, and possible silent neurotoxicity, at different life stages in the zebrafish model. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria. The data management plan for the program can be found here. WHCOHH largerWorkCitation program WHCOHH - Cellular and Molecular Mechanisms Underlying Long-Term Effects of Early Life Exposure to HAB Toxins https://osprey.bco-dmo.org/project/818424 WHCOHH - Cellular and Molecular Mechanisms Underlying Long-Term Effects of Early Life Exposure to HAB Toxins <p>The <strong><em>overall objective</em></strong> of the proposed research is to elucidate the cellular and molecular mechanisms by which early-life exposure to domoic acid (DA) and saxitoxin (STX)— HAB toxins with demonstrated human exposures—can cause neurobehavioral abnormalities later in life.  Most HAB toxins are known to be acutely toxic, causing severe neurotoxicity soon after exposure to high doses. However, there is also extensive and possibly growing human exposure to HAB toxins at low levels that do not cause obvious acute signs of toxicity. Accumulating epidemiological and experimental evidence indicates that exposures during early life can have a profound effect on health later in life (the <em>developmental origins of adult health and disease</em> hypothesis).  In rodents early life exposure to low levels of neuro-active chemicals, including some HAB toxins and chemical pollutants, can cause physiological abnormalities and behavioral defects such as altered cognitive function later in life. However, the mechanisms by which developmental exposure elicits effects in developing animals and later in life are not understood. DA and STX act on ionotropic glutamate receptors and voltage-gated sodium channels, respectively. Both of these protein families are expressed widely in the developing nervous system and critical to establishing proper neuronal function in the central nervous system. <em>The <strong>central hypothesis</strong> of the proposed research is that early life exposure to HAB toxins alters neurotransmitter receptors and ion channels changing prenatal programming of neurodevelopment, leading to altered gene expression and functional changes in neuronal and glial cells in the developing nervous system that ultimately contribute to altered neurobehavioral function in adults.</em>  We will address this hypothesis using zebrafish, a powerful model organism for research on developmental mechanisms including those involved in neurodevelopment and developmental neurotoxicity. Our preliminary research has identified a novel mechanism by which early life exposure to DA disrupts neurodevelopment through effects on myelination. Additional studies demonstrated altered expression of genes involved in axonal extension in embryos exposed to low levels of STX. Linking these studies with past and future HAB occurrence and toxin exposure scenarios (Project 2) will provide an understanding of the long-term health consequences of developmental exposure to HAB toxins, critical for assessing public health risks associated with widespread exposure to these chemicals.</p> WHCOHH HAB toxins largerWorkCitation project eng; USA oceans 2022-01-01 2022-01-01 0 BCO-DMO catalogue of parameters from Genetic accessions, treatment information, and methodology from laboratory experiments studying transcriptomic responses to saxitoxin in zebrafish (Danio rerio) Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 1073 https://darchive.mblwhoilibrary.org/bitstream/1912/29373/1/treatments_accessions.csv download https://doi.org/10.26008/1912/bco-dmo.881469.1 download onLine dataset &lt;p&gt;Adult zebrafish (Tupfel-Long fin wild type strain) were raised under ambient conditions (temperature 28.5 degrees, photoperiod 10:14 light/dark) in Redfield zebrafish facility. Embryos used in the experiment were obtained by tank breeding of the adults. Embryos were injected with saxitoxin or vehicle control at 6 hours post-fertilization.&lt;br /&gt; &lt;br /&gt; Zebrafish embryos were exposed to saxitoxin (STX; 24 or 48 pg) or vehicle (0.3 mM HCl) at 6 hours post fertilization (hpf) via microinjection. We examined transcriptional profiles in embryos at 24, 36 and 48 hpf using RNA sequencing.&lt;br /&gt; &lt;br /&gt; &lt;strong&gt;Sampling and analytical procedures:&lt;/strong&gt;&lt;br /&gt; Total RNA was isolated from embryos at 3 developmental time points and RNAseq was carried out using Illumina platform.&lt;br /&gt; &lt;br /&gt; &lt;strong&gt;Organism scientific name:&lt;/strong&gt; Danio rerio&lt;br /&gt; LSID (Life Sciences Identifier) = urn:lsid:marinespecies.org:taxname:1026595&lt;br /&gt; NCBI:txid903980&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;RNAseq data was pre-processed and mapped to the zebrafish genome (GRCz10) using STAR aligner. HTseq-count was used to obtain read counts. Statistical analysis was done using edgeR.&lt;/p&gt; Specified by the Principal Investigator(s) asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Illumina HiSeq 2000 Illumina HiSeq 2000 PI Supplied Instrument Name: Illumina HiSeq 2000 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.