Abstract:
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.
Keywords:
biomineralisation, developmental biology, mollusc, transcriptomics
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
| Access Constraints: | There are no access constraints. |
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| Use Constraints: | This data is governed by the NERC data policy http://www.nerc.ac.uk/research/sites/data/policy/ and supplied under Open Government Licence v.3 http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/. |
| Creation Date: | 2022-02-11 |
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| Dataset Progress: | Planned |
| Dataset Language: | English |
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| Personnel: | |
| Name | UK Polar Data Centre |
| Role(s) | Metadata Author |
| Organisation | British Antarctic Survey |
| Name | Dr Victoria A Sleight |
| Role(s) | Investigator, Technical Contact |
| Organisation | School of Biological Sciences, University of Aberdeen |
| Name | Prof Melody S Clark |
| Role(s) | Investigator |
| Organisation | British Antarctic Survey |
| Name | Alessandro Cavallo |
| Role(s) | Investigator |
| Organisation | MRC Weatherall Institute of Molecular Medicine |
| Parent Dataset: | N/A |
| Reference: | British Antarctic Survey. Laternula elliptica developmental biology. 2022/02. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA803976. NCBI:BioProject: PRJNA803976. Cavallo, A., Clark, M. S., Peck, L. S., Harper, E. M., & Sleight, V. A. (2022). Evolutionary conservation and divergence of the transcriptional regulation of bivalve shell secretion across life history stages. BioRxiv. https://doi.org/10.1101/2022.04.22.489168 Victoria A. Sleight (2022). Antarctic Clam Laternula elliptica bulk RNAseq developmental stages. BioStudies, S-BSST926. Retrieved from https://www.ebi.ac.uk/biostudies/studies/S-BSST926 |
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| 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. |
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| Lineage: | 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. |
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| Temporal Coverage: | |
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| Start Date | 2018-04-25 |
| End Date | 2018-09-25 |
| Spatial Coverage: | |
| Latitude | |
| Southernmost | -67.56667 |
| Northernmost | -67.56667 |
| Longitude | |
| Westernmost | -68.13333 |
| Easternmost | -68.13333 |
| Altitude | |
| Min Altitude | N/A |
| Max Altitude | N/A |
| Depth | |
| Min Depth | 5m |
| Max Depth | 20m |
| Location: | |
| Location | Antarctica |
| Detailed Location | Hangar Cove, Rothera Point, Adelaide Island, Ryder Bay |
| Data Collection: | Instrumentation: Sequencing: TruSeq Stranded mRNA libraries sequenced on an Illumina NextSeq500 Assembly: Trinity v.2.2.0 Analysis: edgeR and WGCNA |
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| Data Storage: | This data archive includes results files relating to the analysis of Laternula elliptica developmental transcriptomics data. There are two main directories as follows: -WGCNA -edgeR_DE Below is a brief outline of the contents in each directory: -WGCNA This directory includes two further subdirectories: -Annotations This directory includes annotation (swissprot human) table for genes in each module (.csv) -Enrichment_analysis_results A .csv file for each module's enrichment results is included as well as a network file "String_analysis_modules.cys" which can be opened using the free software Cytoscape that shows the results in String-DB network view -edgeR_DE This directory includes a .csv file containing the results of each of the pairwise differential gene expression analyses |
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