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Status |
Public on Jan 03, 2011 |
Title |
T. nigroviridis gills_control 12h |
Sample type |
SRA |
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Source name |
Gills, exposed to control water containing 2.9 mM Ca2+, 12h
|
Organism |
Tetraodon nigroviridis |
Characteristics |
common name: green spotted puffer fish origin: wild, imported from Thailand stage: adult body weight: 4.4±1.6g gender: both
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Biomaterial provider |
Local pet shop
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Treatment protocol |
Acclimatized fish (natural water at 10 ppt salinity, 2.9 mM Ca2+) were transferred to artificial water at 10 ppt containing 2.9mM Ca2+ (control group). Gills were collected 12h after transfer.
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Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was extracted from individual gills with TRI Reagent (Sigma-Aldrich, Madrid, Spain)and polyA RNA purified from pooled total RNA (250 µg) for each experimental group using the Oligotex mRNA Mini Kit (Qiagen, Hilden, Germany). Libraries were constructed using the SuperSAGE procedure by Matsumura et al. 2003 (Gene expression analysis of plant host-pathogen interactions by SuperSAGE. PNAS 100(26):15718-23), with adaptations to massively parallel pyrosequencing described in Terauchi et al. 2008 (SuperSAGE: the most advanced transcriptome technology for functional genomics. In: Handbook of Plant Functional Genomics: Concepts and Protocols. Edited by Kahl G, Meksem K. John Wiley & Sons, NY). Ditags were directly sequenced by pyrosequencing using a GS20 sequencer (454 Life Sciences, Branford, CT, USA).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
454 GS FLX |
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|
Description |
anchor: NlaIII tag_length: 22 tag_count: 2267996 This sample was used for the comparison with the gills of fish transferred to artificial water with control (2.9 mM), low (0.01 mM) or high (10 mM) Ca2+ concentrations for 2 or 12h.
|
Data processing |
Tag extraction and counting was performed with SuperSAGE Perl scripts by Terauchi et al. 2008 (SuperSAGE: the most advanced transcriptome technology for functional genomics. In: Handbook of Plant Functional Genomics: Concepts and Protocols. Edited by Kahl G, Meksem K. John Wiley & Sons, NY).
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Submission date |
Jan 12, 2010 |
Last update date |
Jun 11, 2013 |
Contact name |
Patricia I. S. Pinto |
E-mail(s) |
ppinto@ualg.pt
|
Fax |
+351-289-800069
|
Organization name |
Centro de Ciências do Mar (CCMAR), CIMAR-Laboratório Associado
|
Lab |
Laboratory of comparative and molecular endocrinology (CME)
|
Street address |
Ed.7, University of Algarve, Campus de Gambelas
|
City |
Gambelas |
ZIP/Postal code |
8005-139 Faro |
Country |
Portugal |
|
|
Platform ID |
GPL9947 |
Series (1) |
GSE19854 |
Global gene expression analysis of green spotted puffer fish gills in response to environmental calcium changes |
|
Relations |
BioSample |
SAMN02196547 |