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Transcriptomic Response of Juvenile Red King Crab, Paralithodes Camtschaticus, to the Interactive Effects of Ocean Acidification and Warming (NCEI Accession 0170754)


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            title:  Transcriptomic Response of Juvenile Red King Crab, Paralithodes Camtschaticus, to the Interactive Effects of Ocean Acidification and Warming (NCEI Accession 0170754)
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                date:  2019-04-18
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        abstract:  Impacts of elevated carbon dioxide on marine ecosystems depend on physiological responses to consequential decreased pH and increased temperature. Responses to these environmental factors vary among species and life stages, and interactive effects can be significant. To study effects of decreased pH and increased temperature on juvenile red king crab (RKC, Paralithodes camtschaticus) we exposed individuals to three levels of temperature: 11 degrees Celsius (ambient), 13 degrees Celsius, and 14 degrees Celsius, crossed with three levels of pH: 8.0, 7.8 and 7.5, for a total of nine treatments. To better understand the effect of these environmental changes at the level of genome regulation, we analyzed total RNA of whole crabs using Illumina-based RNA-seq whole-transcriptome sequencing. We assembled a RKC transcriptome using Trinity, annotated the transcriptome using Trinotate, and estimated expression levels using bowtie2, samtools and eXpress. Differentially expressed genes were identified using EdgeR. Genes were clustered by expression patterns. Interactive effects were determined by comparing sets of differentially expressed genes using three statistical models to examine the effect of temperature, the effect of pH, and the interaction between temperature and pH in EdgeR. The largest set of differentially expressed genes encoded proteins involved in regulation of extracellular and cuticular structures, including chitin-binding and calcification related proteins.
        purpose:  This dataset is available to the public for a wide variety of uses including scientific research and analysis.
        credit:  Funding Information: NOAA Ocean Acidification Program (AFSC-Alaska king crab genomics, OAPFY11.01.AFSC.003)
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                            linkage: https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords
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                            name:  GCMD Keyword Forum Page
                            description:  Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 17. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords
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            keyword:  Bering Sea
            keyword:  Kodiak Laboratory
            type:  (MD_KeywordTypeCode) place
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                title:  Provider Geographic Names
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            otherConstraints:  Cite as: Stillman, Jonathon H.; Fay, Scott A.; Swiney, Katherine M.; Foy, Robert J. (2019). Transcriptomic Response of Juvenile Red King Crab, Paralithodes Camtschaticus, to the Interactive Effects of Ocean Acidification and Warming (NCEI Accession 0170754). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://doi.org/10.25921/gv7k-9315. Accessed [date].
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            useLimitation:  Distribution liability: NOAA and NCEI make no warranty, expressed or implied, regarding these data, nor does the fact of distribution constitute such a warranty. NOAA and NCEI cannot assume liability for any damages caused by any errors or omissions in these data. If appropriate, NCEI can only certify that the data it distributes are an authentic copy of the records that were accepted for inclusion in the NCEI archives.
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            otherConstraints:  Use liability: NOAA and NCEI cannot provide any warranty as to the accuracy, reliability, or completeness of furnished data. Users assume responsibility to determine the usability of these data. The user is responsible for the results of any application of this data for other than its intended purpose.
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                title:  NOAA National Centers for Environmental Information (2022). Ocean Carbon and Acidification Data System (OCADS). NOAA National Centers for Environmental Information. https://www.ncei.noaa.gov/products/ocean-carbon-acidification-data-system
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                    date:  2022-04
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                      Anchor:  https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/1730 NOAA National Centers for Environmental Information
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                      Anchor:  https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/1730 US DOC; NOAA; NESDIS; National Centers for Environmental Information (NCEI)
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                otherCitationDetails:  [accessed 2024-02-08]
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                        voice:  +1-301-713-3277
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                        electronicMailAddress:  NCEI.Info@noaa.gov
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                fees:  In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
                orderingInstructions:  Contact NCEI for other distribution options and instructions.
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                description:  NCEI Accession 0170754 v1.1 was published.
                dateTime:
                  DateTime:  2019-04-18T20:55:21Z
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                        title:  NCEI Accession 0170754 v1.1
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                                    linkage: https://www.ncei.noaa.gov/archive/accession/0170754/1.1
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                                    name:  NCEI Accession 0170754 v1.1
                                    description:  published 2019-04-18T20:55:21Z
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                description:  Parameter or Variable: Dissolved Inorganic Carbon; Abbreviation: DIC; Unit: umol/kg; Observation type: Laboratory Experiment; In-situ / Manipulation / Response variable: Manipulation condition.
            processStep:  (LE_ProcessStep)
                description:  Parameter or Variable: Total alkalinity; Abbreviation: TA; Unit: umol/kg; Observation type: Laboratory Experiment; In-situ / Manipulation / Response variable: Manipulation condition.
            processStep:  (LE_ProcessStep)
                description:  Parameter or Variable: pH; Abbreviation: pH; pH scale: Total; Observation type: Laboratory Experiment; In-situ / Manipulation / Response variable: Manipulation condition; At what temperature was pH reported: variable.
            processStep:  (LE_ProcessStep)
                description:  Parameter or Variable: Fragments Per Kilobase of transcript per Million mapped reads; Abbreviation: FPKM; Unit: Median Centered Log2 transformed count; Uncertainty: maximumFPKM minus the minimumFPKM was less than or equal to 3.0 to reduce clustering uncertainty.
            processStep:  (LE_ProcessStep)
                description:  Parameter or Variable: Temperature; Abbreviation: Temp; Unit: degree Celsius.
            processStep:  (LE_ProcessStep)
                description:  Parameter or Variable: Salinity; Abbreviation: Salinity; Unit: PSU .
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        maintenanceNote:  Metadata are developed, maintained and distributed by NCEI. Updates are performed as needed to maintain currentness.
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            organisationName:  NOAA National Centers for Environmental Information
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