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 Overall Abstract: The Woods Hole Center for Oceans and Human Health (WHCOHH) will comprise a strong and integrated set of research projects using novel in situ sampling technologies and modeling approaches building on prior research to address how environmental factors influence harmful algal bloom (HAB) dynamics and human exposure to HAB toxins, a serious and global human health threat. The overall objective is to protect public health through enhanced understanding of how oceanic processes affect the intensity and distribution of toxin-producing HABs and to understand the potential health risks from exposure even to low levels of their potent neurotoxins, especially during susceptible stages of life. The Center will focus on two key HAB taxa: Alexandrium catenella, which produces the saxitoxins responsible for paralytic shellfish poisoning (PSP), and Pseudo-nitzschia spp., which produce domoic acid responsible for amnesic shellfish poisoning (ASP) syndrome, both are expanding geographically. Novel, targeted, efficient, and data-rich sampling approaches developed by the applicants and applied in situ in natural settings have revealed new controls of A. catenella population dynamics, and have identified possible new environmental links regarding toxic Pseudo-nitzschia species. Project 1 will examine further the physiological and environmental variables affecting these HABs, which may underlie population adaptation in different habitats and different environmental regimes. Project 2 will incorporate these new and fundamental insights on bloom regulation into coupled population models to predict HAB events, a key step toward being able to quantify future risks from this recurrent public health threat. In biomedical studies with the zebrafish model, Project 3 has identified myelination in the developing brain as a target of domoic acid. They will use transgenic zebrafish and single-cell RNA-sequencing to identify the cell-specific mechanisms underlying effects of domoic acid, saxitoxin, and the cyanotoxin anatoxin-a in zebrafish embryos in vivo and will use human iPSC-derived 3D brain systems in vitro to elucidate toxin effects on neural and glial cell differentiation in human cells. Studies also will determine whether prior exposure to ubiquitous persistent organic pollutants may modify effects of subsequent exposure to saxitoxin and domoic acid. All projects will collaborate to link oceanic processes to human exposure, helping to define the exposure of susceptible human subpopulations. The Community Engagement Core will facilitate integration of the research with education and engagement of resource managers and other stakeholders. We also will improve awareness of emerging HAB issues for the public health community and develop new educational materials and interactive activities for K-12 classrooms, and for health care providers. An Administrative Core will encourage open discussion of planning, integration, and communication, and provide rigorous evaluation of progress in all aspects of the program. NSF Award Abstract: See https://www.nsf.gov/awardsearch/show-award?AWD_ID=2418297 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 overall objective of the proposed research is to elucidate the cellular and molecular mechanisms of toxicity from developmental exposure to harmful algal bloom (HAB) toxins. The HAB toxins domoic acid (DA), saxitoxin (STX), and anatoxin-a (ATX-a) occur in marine and coastal water bodies as well as in food sources and pose a significant threat to public health. Current regulatory guidelines for HAB toxins in seafood are designed to protect against acute exposure to adults. However, seafood with HAB toxins below the regulatory limits is regularly harvested and the consequences of exposure to low levels of HAB toxins particularly to children and young adults are not well understood. It is well known that the early life environment can profoundly influence health throughout the life course (the developmental origins of health and disease concept). The central hypothesis of the proposed research is that exposure to HAB toxins during early development alters various neuronal and glial cell types independently, leading to cell-type specific transcriptional changes, ultimately contributing to altered neurobehavioral outcomes. We propose to test this hypothesis using two complementary model systems: zebrafish, an established model organism for characterizing molecular, cellular, and behavioral changes <em>in vivo</em>, and human iPSC-derived 3D brain systems <em>in vitro</em> for elucidating the effects of toxins on differentiating human neural cells. In Aim 1, we will use transgenic zebrafish embryos and single-cell RNA sequencing to investigate the cellular and molecular mechanisms underlying the neurodevelopmental toxicity of DA, STX, and ATX-a. Building on our previous studies, in Aim 1.1 we will test the hypothesis that DA exposure of zebrafish embryos affects oligodendrocyte-neuron interactions in part by targeting oligodendrocytes that are necessary for the maturation and survival of axons. In Aim 1.2, we will test the hypothesis that STX exposure during development alters extracellular matrix at the synapses in the brain, with impacts on neural circuit formation in larvae. In Aim 1.3, we will test the hypothesis that developmental exposure of zebrafish embryos to ATX-a causes nervous system deficits by activating nicotinic acetylcholine receptors. In Aim 2, using human iPSC-derived neuronal cultures, we will investigate the effects on exposure to HAB toxins on mechanisms of neuronal and glial cell differentiation. In Aim 3, we will test the hypothesis that combined early life and preconceptional exposure to low levels of PCBs influences the responses to HAB toxins. In Aim 4, we will use probabilistic models to assess human exposure to DA during susceptible windows of development and collaborate with Project 1, 2 and CEC to use coupled HAB biophysical models and exposure models to predict human exposure to STX and DA. Overall, the results from this research will contribute to improved understanding of the potential health consequences of developmental exposure to HAB toxins in humans, critical for assessing public health risks associated with the possibly increasing exposure to these toxins.</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.