Click here to view this collection in the new DAP user interface
Raw reads and final assembled contigs for pennate diatom project
Raw sequencing reads and final assembled contigs associated with the 454 sequencing of the toxicant responsive transcriptome of the diatom Ceratoneis closterium. This species often is also often referred to by its previous names, Nitzschia closterium and Cylindrotheca closterium. It is species CS-5 in the CSIRO Collection of Living Microalgae, Mari... morene and Atmospheric Research, Hobart, Australia. Original .fasta and .qual files are included, as well as the contigs associated with the final assembly as desribed in the paper (Hook et al., to be submitted, BMC Genomics)
Environmental Science and Management not elsewhere classified
Next generation sequencing
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 and Merrin S Adams conceived of and designed the study; Sharon E Hook, Merrin S Adams, and Marc Wilkins (UNSW) obtained funding; Francesca Gissi and Hannah L Osborn conducted culturing, toxicological exposures and algal collection;Hannah L Osborn conducted molecular biological laboratory work; Sharon E Hook, Natalie Twine (UNSW), Philippe Moncuquet and Marc Wiilkins analyzed the data; Sharon E Hook, Merrin S Adams, Hannah L Osborn, 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
Hook, Sharon; Osborn, Hannah; Gissi, Francesca; Moncuquet, Philippe; Twine, Natalie; Wilkins, Marc; Adams, Merrin (2013): Raw reads and final assembled contigs for pennate diatom project. v1. CSIRO. Data Collection.
All Rights (including copyright) CSIRO Australia 2013.
The metadata and files (if any) are available to the public.
1177.2 Estuarine Health Assessment
Metabarcoding of Copper Contaminated Sediments
Manipulative experiment using whole benthic communities obtained from an estuary in Rhode Island, USA.
Roche 454 FLX Titanium
Others were also interested in