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

01 Jul 2010

05 Jun 2014

CSIRO Enquiries
1300 363 400

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


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.

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


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


Roche 454 FLX Titanium

Sharon Hook

Emma Johnston

Sham Nair

Anthony Roach

Philippe Moncuquet

Natalie Twine

Marc Wilkins

David Raftos

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