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RNASeq files for fish health in the Tully and Daintree rivers

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About this Collection

RNASeq files for fish health in the Tully and Daintree rivers


These files illumina sequencing reads representing the hepatic transcriptome of wild caught barramundi from the Daintree River (fish numbers 2-7) or the Tully River (fish numbers 97-104).


Environmental Sciences not elsewhere classified Gene Expression (incl. Microarray and other genome-wide approaches)


https://doi.org/10.4225/08/55E799BA0F73E


2011


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fish health cortisol stress herbicide pesticide RNA transcriptome


The Ramaciotti Centre for Gene function analysis at the University of NSW performed the cDNA library preparation, and the samples were run at the Garvan Institute (Figure 1). The samples were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), using 1 µg of total RNA as input. The libraries were enriched using 13 cycles of PCR and the insert size ranged from 80-330 base pairs, with a median at 150 bp. Fourteen libraries were multiplexed in one lane of the HiSeq2500 and sequenced using TruSeq v4 SBS reagents and 125 bp paired-end reads.


Funding for this research was provided by both the Land and Water and by the Oceans and Atmosphere Flagships in CSIRO. Computational support was provided by the bioinformatics core at CSIRO Computational Informatics. Sequencing was provided by the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales. The authors would like to thank Dean Jones (formerly CSIRO) for assistance with the sample collection, Drs. Helen Spiers, Helena Mangs and Tonia Russell of the University of NSW and Francesca Gissi (CSIRO) for technical assistance. Drs Brad Angel, Graeme Batley and Peter Bain of the CSIRO Land and Water Flagship for valuable discussions.


Creative Commons Attribution 3.0 Unported Licence


Australian Institute of Marine Sciences (Australia), CSIRO (Australia), Queensland Department of Science, Information Technology, Innovation and the Arts (DSITIA) (Australia)


CSIRO; Kroon, Frederieke; Metcalfe, Suzanne; Greenfield, Paul; Moncuquet, Philippe; McGrath, Annette; Smith, Rachel; Warne, Michael; Turner, Ryan; McKeown, Adam; Westcott, David (2015): RNASeq files for fish health in the Tully and Daintree rivers. v1. CSIRO. Data Collection. https://doi.org/10.4225/08/55E799BA0F73E


All Rights (including copyright) CSIRO Australia 2015.


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

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About this Project

Estuarine Health Assessment


To investigate potential impacts of declining water quality on fish physiology, RNASeq was used to characterize and compare the hepatic transcriptomes of barramundi (Lates calcarifer) captured from two of these tropical river catchments in Queensland, Australia.


Sharon Hook


Next generation sequencing


To investigate potential impacts of declining water quality on fish physiology, RNASeq was used to characterize and compare the hepatic transcriptomes of barramundi (Lates calcarifer) captured from two of these tropical river catchments in Queensland, Australia.


Experiment


CSIRO


Frederieke Kroon


Suzanne Metcalfe


Paul Greenfield


Philippe Moncuquet


Annette McGrath


Rachel Smith


Michael Warne


Ryan Turner


Adam McKeown


David Westcott


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