Date (Creation)

2022-02-11

Date (Revision)

2022-02-11

Date (Publication)

2022-02-11

Date (released)

2022-02-11

Edition

1.0

Unique resource identifier

https://doi.org/10.5285/6cd12de1-02c7-4f94-86f0-c11e76b86067

Codespace

doi

Unique resource identifier

GB/NERC/BAS/PDC/01607

Codespace

https://data.bas.ac.uk/

Unique resource identifier

NE/J500173/1

Codespace

award

Other citation details

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

Credit

No credit.

Status

Completed

Point of contact

Organisation name	Individual name	Electronic mail address	Role
School of Biological Sciences, University of Aberdeen	Sleight, Victoria A		Author
British Antarctic Survey	Clark, Melody S		Author
MRC Weatherall Institute of Molecular Medicine	Cavallo, Alessandro		Author
NERC EDS UK Polar Data Centre		PDCServiceDesk@bas.ac.uk	Point of contact

Maintenance and update frequency

As needed

Maintenance note

Completed

Global Change Master Directory (GCMD) Science Keywords

• EARTH SCIENCE > Biosphere > Animal Taxonomy > Mollusks

Theme

• biomineralisation

• developmental biology

• mollusc

• transcriptomics

Place

• Hangar Cove, Rothera Point, Adelaide Island, Ryder Bay Antarctica

GEMET - INSPIRE themes, version 1.0

• Habitats and biotopes

Access constraints

Other restrictions

Other constraints

no limitations to public access

Access constraints

Other restrictions

Other constraints

no limitations

Use constraints

License

Other constraints

Open Government Licence v3.0

Use constraints

Other restrictions

Other constraints

This data is governed by the NERC Data Policy: https://www.ukri.org/who-we-are/nerc/our-policies-and-standards/nerc-data-policy/

Use constraints

Other restrictions

Other constraints

This data is governed by the NERC data policy and supplied under Open Government Licence v.3

Use constraints

Other restrictions

Other constraints

There are no access constraints.

Unique resource identifier

url

Codespace

url

Association Type

Cross reference

Unique resource identifier

url

Codespace

url

Association Type

Cross reference

Unique resource identifier

url

Codespace

url

Association Type

Cross reference

Unique resource identifier

url

Codespace

url

Association Type

Cross reference

Spatial representation type

Text, table

Language

English

Character set

UTF8

Topic category

• Biota

Begin date

2018-04-25

End date

2018-09-25

Supplemental Information

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.

Title

European Petroleum Survey Group (EPSG) Geodetic Parameter Registry

Date (Publication)

2008-11-12

Cited responsible party

Organisation name	Individual name	Electronic mail address	Role
European Petroleum Survey Group		EPSGadministrator@iogp.org	Publisher

Unique resource identifier

urn:ogc:def:crs:EPSG::3031

Version

6.18.3

Hierarchy level

Dataset

Statement

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.

Metadata

File identifier

6cd12de1-02c7-4f94-86f0-c11e76b86067 XML

Metadata language

English

Character set

UTF8

Hierarchy level

Dataset

Hierarchy level name

dataset

Date stamp

2022-02-11

Metadata standard name

ISO 19115 Geographic Information - Metadata

Metadata standard version

ISO 19115:2003(E)

Metadata author

Organisation name	Individual name	Electronic mail address	Role
NERC EDS UK Polar Data Centre		polardatacentre@bas.ac.uk	Point of contact