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Paratya australiensis protein-coding transcriptome

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About this Collection

Paratya australiensis protein-coding transcriptome


A collection of DNA and deduced protein sequences corresponding to the protein-coding transcriptome of adult specimens of the freshwater atyid shrimp Paratya australiensis. The sequences are derived from specimens from a laboratory-based experiment involving the exposure of shrimp to drain water from a site affected by acidification due to oxidatio... more


Environmental Sciences not elsewhere classified


https://doi.org/10.4225/08/58046aaadaeda


2013


2016


Peter Bain
Peter.Bain@csiro.au

Aquatic toxicology acid sulfate soils prawns schrimp gene expression RNA-Seq next-generation DNA sequencing


Total RNA was isolated from control specimens and specimens exposed to acid drainage water and mRNA was sequenced by a service provider using an Illumina HiSeq2000 instrument. Library preparation was strand-specific and sequences were generated using paired-end mode with 100 cycles. Putative transcripts were assembled in a de novo fashion (without a reference genome) using Trinity software (v. 2.0.6). Protein sequences were deduced using Transdecoder software (v. 2.0.1). Likely descriptions and functions were assigned using Blast2GO command-line v. 1.0.2.


Anu Kumar conceived the project, Deb Gonzago performed laboratory exposures, Peter Bain isolated RNA and performed all bioinformatics analyses, Adrienne Gregg validated selected changes in transcript abundance inferred from RNA-Seq using alternative methods (q-RT-PCR).


CSIRO Data Licence


CSIRO (Australia)


Bain, Peter; Kumar, Anu; Gregg, Adrienne (2016): Paratya australiensis protein-coding transcriptome. v1. CSIRO. Data Collection. https://doi.org/10.4225/08/58046aaadaeda


All Rights (including copyright) CSIRO 2016.


The metadata and files (if any) are available to the public.

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About this Project

CLSDApprop -Ecotoxi Risk/C2012/7814


Ecotoxicological risk assessment in complex environmental systems: linking contaminant mobilisation, transport and impacts


Paul Shand


RNA-Seq and transcriptome assembly of Paratya australiensis exposed to acid sulfate drainage water


Sequencing and assembly of messenger RNA from adult Paratya australiensis exposed to acid sulfate drainage water (and control specimens exposed to river water)


Experiment


Illumina HiSeq 2000


Peter Bain


Anu Kumar


Adrienne Gregg


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