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Sample GSM495813 Query DataSets for GSM495813
Status Public on Jan 03, 2011
Title T. nigroviridis gills_control 12h
Sample type SRA
 
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
Biomaterial provider Local pet shop
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.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model 454 GS FLX
 
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).
 
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

Data table header descriptions
SEQUENCE
COUNT
TPM tags per million

Data table
SEQUENCE COUNT TPM
TTCGGGGAACTGACAGTCGCAC 582 8559.33
TTGGTGTCCGCAAGGGTAGAGA 566 8324.02
GTTGCTTCAATAAAATCACCAA 493 7250.43
TATTCCTACTGAGGTGATGCGT 316 4647.33
TCATAGCTGCTCACTGCTAAAT 285 4191.42
GACCATAATGTTATAACAAGCT 236 3470.79
GGATTCGGTCTCTTTGATTAAT 226 3323.72
AAAAGAATTGTTCTGCTTTTAT 213 3132.54
TCTGAATTATGCCTCGGTGACA 198 2911.94
TCAAAGCAATAAAAGCCTCAGT 196 2882.52
TTTGACATTAAAAGATCTGTGA 190 2794.28
GAGCCTATTAAACGAACTGTGG 185 2720.75
GGCAAACCCCAGCGTCTCTATT 179 2632.51
AACTTCAGGACACCCAGAGGAG 177 2603.09
AAATAAAGACAAAGTGAAGCAA 173 2544.27
AAGGTCAGCGCTCCCCGCGTGG 157 2308.96
TTCGGGGAACTGGTGACTGCAC 154 2264.84
TGGCACTCATCTTTGCTGCTGG 153 2250.13
AACTTTTGCTATCAATAAACTG 151 2220.72
CAGGCAGCTTCCTCATAAACAC 138 2029.53

Total number of rows: 27403

Table truncated, full table size 831 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Raw data provided as supplementary file

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