6cd12de1-02c7-4f94-86f0-c11e76b86067 eng utf8 dataset dataset NERC EDS UK Polar Data Centre +44 (0)1223 221400 British Antarctic Survey, High Cross, Madingley Road Cambridge Cambridgeshire CB3 0ET United Kingdom polardatacentre@bas.ac.uk https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/ information pointOfContact 2022-02-11 ISO 19115 Geographic Information - Metadata ISO 19115:2003(E) European Petroleum Survey Group (EPSG) Geodetic Parameter Registry 2008-11-12 publication European Petroleum Survey Group EPSGadministrator@iogp.org https://www.epsg-registry.org/ EPSG Geodetic Parameter Dataset The EPSG Geodetic Parameter Dataset is a structured dataset of Coordinate Reference Systems and Coordinate Transformations, accessible through this online registry. information publisher urn:ogc:def:crs:EPSG::3031 6.18.3 Laternula elliptica developmental bulk RNA-Seq data analysis results 2022, collected from Hangar Cove Rothera Point, on Adelaide Island in 2018 2022-02-11 creation 2022-02-11 revision 2022-02-11 publication 2022-02-11 released 1.0 https://doi.org/10.5285/6cd12de1-02c7-4f94-86f0-c11e76b86067 doi GB/NERC/BAS/PDC/01607 https://data.bas.ac.uk/ NE/J500173/1 award Please cite this item as: Sleight, V., Clark, M., & Cavallo, A. (2022). Laternula elliptica developmental bulk RNA-Seq data analysis results 2022, collected from Hangar Cove Rothera Point, on Adelaide Island in 2018 (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/6cd12de1-02c7-4f94-86f0-c11e76b86067 This dataset comprises mRNA that was extracted from Laternula elliptica developmental stages (blastula to juvenile) and sequenced (n=3 pools of 200 individual per stage). The resulting sequence data was analysed and the following results files and analysis scripts are available here: Results files from differential gene expression analysis in edgeR (edgeR_DE), results files from WGCNA analysis (WGCNA). Data collection was carried out over Hangar Cove Rothera Point, Adelaide Island, in Ryder Bay, from 2018-04-25 to 2018-09-25 by researchers with the British Antarctic Survey. The data was collected as part of research on the developmental biology of molluscs. This work was supported by UKRI Natural Environment Research Council (NERC) Core Funding to the British Antarctic Survey, a DTG Studentship (Project Reference: NE/J500173/1) and a Junior Research Fellowship to VAS from Wolfson College, University of Cambridge. No credit. completed Sleight, Victoria A School of Biological Sciences, University of Aberdeen Researcher author Clark, Melody S British Antarctic Survey Researcher author Cavallo, Alessandro MRC Weatherall Institute of Molecular Medicine Researcher author NERC EDS UK Polar Data Centre +44 (0)1223 221400 British Antarctic Survey, High Cross, Madingley Road Cambridge Cambridgeshire CB3 0ET United Kingdom PDCServiceDesk@bas.ac.uk https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/ information pointOfContact asNeeded completed EARTH SCIENCE > Biosphere > Animal Taxonomy > Mollusks theme Global Change Master Directory (GCMD) Science Keywords 2026-01-27 publication 23 Global Change Data Center, Science and Exploration Directorate, Goddard Space Flight Center (GSFC) National Aeronautics and Space Administration (NASA) Greenbelt MD United States of America https://earthdata.nasa.gov/about/gcmd/global-change-master-directory-gcmd-keywords Global Change Master Directory (GCMD) Keywords The information provided on this page seeks to define how the GCMD Keywords are structured, used and accessed. It also provides information on how users can participate in the further development of the keywords. information publisher biomineralisation developmental biology mollusc transcriptomics theme Hangar Cove, Rothera Point, Adelaide Island, Ryder Bay Antarctica place Habitats and biotopes theme GEMET - INSPIRE themes, version 1.0 2021-01-06 revision otherRestrictions no limitations to public access otherRestrictions no limitations license Open Government Licence v3.0 otherRestrictions This data is governed by the NERC Data Policy: https://www.ukri.org/who-we-are/nerc/our-policies-and-standards/nerc-data-policy/ otherRestrictions This data is governed by the NERC data policy and supplied under Open Government Licence v.3 otherRestrictions There are no access constraints. url url crossReference url url crossReference url url crossReference url url crossReference textTable eng utf8 biota -68.13333 -68.13333 -67.56667 -67.56667 2018-04-25 2018-09-25 It is recommended that careful attention be paid to the contents of any data, and that the author be contacted with any questions regarding appropriate use. If you find any errors or omissions, please report them to polardatacentre@bas.ac.uk. NERC EDS UK Polar Data Centre +44 (0)1223 221400 British Antarctic Survey, High Cross, Madingley Road Cambridge Cambridgeshire CB3 0ET United Kingdom PDCServiceDesk@bas.ac.uk https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/ information distributor text/csv text/plain text/csv text/plain bytes 113246208 https://ramadda.data.bas.ac.uk/repository/entry/show?entryid=6cd12de1-02c7-4f94-86f0-c11e76b86067 WWW:LINK-1.0-http--link Get Data Download data download bytes 113246208 https://ramadda.data.bas.ac.uk/repository/entry/show?entryid=6cd12de1-02c7-4f94-86f0-c11e76b86067 WWW:LINK-1.0-http--link Get Data Download data download bytes 113246208 https://www.ncbi.nlm.nih.gov/bioproject/PRJNA803976/ WWW:LINK-1.0-http--link Get Data Download data download bytes 113246208 https://www.ncbi.nlm.nih.gov/bioproject/PRJNA803976/ WWW:LINK-1.0-http--link Get Data Download data download dataset Methodology: Adult L. elliptica were collected from Hangar Cove Rothera Point, Adelaide Island, Ryder Bay between 2018-04-25 and 2018-09-25 and transported in a refrigerated recirculating aquarium by ship to the British Antarctic Survey aquarium facility (Cambridge, UK). Embryos were obtained from an adult broodstock of sexually mature individuals and divided into three independent closed-system 1L tanks. Embryos were maintained at 0 degrees Celsius (within 0.5 degrees Celsius), aerated with an airstone with water changes every two days using autoclaved seawater, until the desired developmental stage. Embryos were staged as per (Peck et al. 2007) and the following stages were studied: blastula, gastrula, trochophore, veliger, early D-larvae (PI), late D-larvae (PII) and postlarva/juvenile (DI). Triplicate RNA-Seq samples were collected for each developmental stage, one from each independent tank. For each sample, two hundred staged-matched embryos were selected, transferred into a microcentrifuge tube, snap frozen in a 70 percent ethanol dry ice slurry and stored at -80 degrees Celsius. Total RNA was extracted from each sample as per manufactures' recommendations (Relia Miniprep kit, Promega) and tested for quality and quantity using Nanodrop and Agilent Tapestation. All samples had a RNA Integrity Number (RIN) of over 7. Libraries were prepared by the sequencing facility in the Biochemistry Department at the University of Cambridge (TruSeq Stranded mRNA, Illumina) and sequenced on an Illumina NextSeq500 generating over 300 million 150bp stranded paired-end reads. Clean, normalised reads were assembled using Trinity v.2.2.0 with default parameters. Transcript abundance was estimated by alignment-based quantification using Trinity v.2.2.0 utilities. Transcripts from each cleaned library were aligned to the transcriptome using bowtie2 with default parameters and transcript abundance estimates were calculated using RNA-Seq by Expectation-Maximization (RSEM). Raw counts and Trimmed Mean of M-values [TMM] normalised Fragments Per Kilobase Of Exon Per Million Fragments Mapped [FPKM] matrices were generated using Trinity v2.2.0 utilities. Pairwise differential gene expression tests were performed to find transcripts that were upregulated at each stage of shell development (compared to the previous stage). Using the EdgeR package, a negative binomial additive general linear model with a quasi-likelihood F-test was performed and p-values were adjusted for multiple testing using the Benjamini-Hochberg method to control the false discovery rate, cut-offs for statistical significance (FDR less than or equal to 0.05) and magnitude were used (log2FC less than 2). Upregulated transcripts were putatively annotated based on sequence similarity searched using blastx against Uniprot (http://www.uniprot.org/), and screened for functional categories relating to gene regulation and shell secretion. For WGCNA analysis, TMM-FPKM values were used to calculate a gene dissimilarity matrix (adjacency= softpower 16 and signed, TOMsimilarity = signed) and hierarchical clustering was performed (method = average). Modules were determined using the cutreeDynamic function with a minimum gene membership threshold of 30 and dynamic tree cut-off of 25. Modules were correlated to external traits (days post fertilisation or candidate gene expression values). Modules of that were significantly correlated to traits of interest were extracted and all transcripts were putatively annotated based on sequence similarity searched using blastx against Uniprot and tested for functional enrichment. Data collection: Instrumentation: Sequencing: TruSeq Stranded mRNA libraries sequenced on an Illumina NextSeq500 Assembly: Trinity v.2.2.0 Analysis: edgeR and WGCNA Data quality: Triplicate RNA-Seq libraries were generated for each developmental stage Raw reads (total 309,593,642) were cleaned using ea-utils tool v1.1.2 fastq-mcf (quality -q 30, and length -l 100), after cleaning 296,480,254 reads remained. asNeeded completed