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Sample GSM589006 Query DataSets for GSM589006
Status Public on Sep 01, 2010
Title Day 10, Normoxia, Susceptible oysters, pool 2
Sample type RNA
 
Channel 1
Source name Pooled Digestive Gland, Susceptible Oysters, 10 day Normoxia
Organism Magallana gigas
Characteristics oyster line: Susceptible Oysters
tissue: Digestive Gland
Treatment protocol Hypoxia exposure maintained for 20 d. The oxygen levels were reduced by bubbling nitrogen to obtain 2 mg O2 L-1 (30% oxygen saturation at 20°C)
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Extract-all Reagent (Eurobio) manufacturer's instructions
Label Cy5
Label protocol Five μg of total RNA were directly labeled by reverse transcription using the Direct ChipShot Direct Labeling and Clean-Up Kit (Promega) according to the manufacturer’s recommendations.
 
Channel 2
Source name Total RNA from pooled entire wild oysters
Organism Magallana gigas
Characteristics oyster line: Wild Oysters
tissue: All Tissues
Treatment protocol Hypoxia exposure maintained for 20 d. The oxygen levels were reduced by bubbling nitrogen to obtain 2 mg O2 L-1 (30% oxygen saturation at 20°C)
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Extract-all Reagent (Eurobio) manufacturer's instructions
Label Cy3
Label protocol Five μg of total RNA were directly labeled by reverse transcription using the Direct ChipShot Direct Labeling and Clean-Up Kit (Promega) according to the manufacturer’s recommendations.
 
 
Hybridization protocol The slides were filled with a pre-hybridization buffer (Chip Spread buffer containing 4× SSC and 0.2% SDS) for 1 h at 42°C. Hybridization was conducted overnight at 42°C in the automatic station according to the manufacturer’s instructions. After hybridization, the arrays were washed twice with Ribowash solution (0.1 M Tris, 0.05 M EDTA, and 0.4 M NaCl) and once with 0.1× SSC, and finally centrifuged (6,000 rpm, 15 s, room temperature) for drying
Scan protocol Microarray slides were scanned using a Genepix 4000B microarray scanner (Axon Instruments Inc.) with standard dual laser excitation at 532 nm (17 mW) and 635 nm (10 mW) according to the following parameters: Cy5 Photo Multiplier Tube (PMT) 550 and Cy3 PMT 590. Images (16-bit TIF) were analyzed using GenePix pro 5.1 software (Axon Instruments Inc.) according to the manufacturer’s instructions
Data processing Microarray data were initially processed using the language R/BioConductor (R Development Core Team 2008). LOESS normalization and background correction were performed with the limma package. Missing (NA) values where calculated with an application of the TMev Software (A.I. Saeed, N.K. Bhagabati, J.C. Braisted, W. Liang, V. Sharov, E.A. Howe, et al., TM4 Microarray Software Suite, in: DNA Microarrays, Part B: Databases and Statistics, Academic Press, 2006: pp. 134-193).
 
Submission date Aug 31, 2010
Last update date Aug 31, 2010
Contact name Rossana Sussarellu
E-mail(s) rossana.sussarellu@ifremer.fr
Organization name Ifremer
Department Ressources Biologiques et Environnement
Lab Laboratoire d'Ecotoxicologie
Street address Rue de l'Ile d'Yeu
City Nantes
ZIP/Postal code 44300
Country France
 
Platform ID GPL8639
Series (1)
GSE23883 Transcriptomic response of the Pacific oyster Crassostrea gigas to hypoxia

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
cdn19p0001a01.f.1 -0.08541333
cdn19p0001a02.f.1 0.11453043
cdn19p0001a03.f.1 0.008530411
cdn19p0001a07.f.1 0.01559113
cdn19p0001a08.f.1 0.10501578
cdn19p0001a09.f.1 0.22286098
cdn19p0001a10.f.1 0.016748862
cdn19p0001a11.f.1 -0.009346603
cdn19p0001a13.f.1 0.03186904
cdn19p0001a14.f.1 0.14812587
cdn19p0001a16.f.1 -0.045703463
cdn19p0001a17.f.1 0.14847264
cdn19p0001a18.f.1 -0.33841035
cdn19p0001a19.f.1 0.10291339
cdn19p0001a20.f.1 -0.08789439
cdn19p0001a21.f.1 0.14501938
cdn19p0001a22.f.1 0.13963807
cdn19p0001a23.f.1 0.006703327
cdn19p0001a24.f.1 -0.05637419
cdn19p0001b01.f.1 0.16329871

Total number of rows: 9058

Table truncated, full table size 290 Kbytes.




Supplementary file Size Download File type/resource
GSM589006.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table
Processed data are available on Series record

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