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Raw reads and final assembled contigs for Sydney rock oyster (Saccostrea glomerata) project

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About this Collection

Raw reads and final assembled contigs for Sydney rock oyster (Saccostrea glomerata) project


Raw sequencing reads and final assembled contigs associated with the 454 pyrosequencing of the stressor associated transcriptome of the gill and digestive gland of the Sydney Rock Oyster (Saccostrea glomerata). Original .fasta and .qual files are included, as well as the final assembly as described in the paper (Hook et al., Marine Genomics, to be... more


Environmental Sciences not elsewhere classified


https://doi.org/10.4225/08/53ED4DFE71DA6


01 Jul 2010


05 Jun 2014


CSIRO Enquiries
CSIROEnquiries@csiro.au
1300 363 400

bivalve ecotoxicology immune response next generation sequencing immune response stress response RNA Seq


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Workflow in Galaxy for data analysis


The reads are the output of 454 pyrosequencing runs performed at the Ramaciotti Centre, UNSW. The contigs were assembled by intitally filtereing the reads for quality using the CSIRO Galaxy instance then by assembling the reads using the MIRA algorithm and the CSIRO Galaxy instance.


Sharon E. Hook Tony Roach (DECCW), Emma L. Johnston (UNSW) and Dave Raftos (Macquarie University) conceived of and designed the study; Sharon E Hook, Emma L. Johnston (UNSW), and Marc Wilkins (UNSW) obtained funding; Emma Johnston and Tony Roach deployed and collected oysters ; Sham Nair exposed oysters to surrogate pathogens; Sharon Hook and Sham Nair conducted molecular biological laboratory work; Sharon E Hook, Natalie Twine (UNSW), Philippe Moncuquet and Marc Wiilkins analyzed the data; Sharon E Hook, Dave Raftos, Sham Nair, Natalie Twine, Philippe Moncuquet and Marc Wilkins interpreted the data; all authors contributed to writing the manuscript. All authors read and approved the final manuscript.


Creative Commons Attribution 3.0 Unported Licence


CSIRO (Australia), Macquarie University (Australia), NSW Dept of Environment, Climate Change & Water (DECCW) (Australia), University of New South Wales (Australia)


Hook, Sharon; Johnston, Emma; Nair, Sham; Roach, Anthony; Moncuquet, Philippe; Twine, Natalie; Wilkins, Marc; Raftos, David (2014): Raw reads and final assembled contigs for Sydney rock oyster (Saccostrea glomerata) project. v1. CSIRO. Data Collection. https://doi.org/10.4225/08/53ED4DFE71DA6


All Rights (including copyright) CSIRO Australia 2014.


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

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About this Project

1177.2 Estuarine Health Assessment


Metabarcoding of Copper Contaminated Sediments


Sharon Hook


Experiment


Manipulative experiment using whole benthic communities obtained from an estuary in Rhode Island, USA.


Experiment


Roche 454 FLX Titanium


Sharon Hook


Emma Johnston


Sham Nair


Anthony Roach


Philippe Moncuquet


Natalie Twine


Marc Wilkins


David Raftos


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