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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... moren and re-wetting of acid sulphate soils. Please see associated publication in BMC Genomics (Bain et al., De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water, BMC Genomics, accepted manuscript). less
Environmental Sciences not elsewhere classified
acid sulfate soils
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
Bain, Peter; Kumar, Anu; Gregg, Adrienne (2016): Paratya australiensis protein-coding transcriptome. v1. CSIRO. Data Collection.
All Rights (including copyright) CSIRO 2016.
The metadata and files (if any) are available to the public.
CLSDApprop -Ecotoxi Risk/C2012/7814
Ecotoxicological risk assessment in complex environmental systems: linking contaminant mobilisation, transport and impacts
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)
Illumina HiSeq 2000
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