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Sample GSM433593 Query DataSets for GSM433593
Status Public on Oct 02, 2009
Title IR-Vt/At-2
Sample type RNA
 
Channel 1
Source name IR-Vt-2
Organism Solea senegalensis
Characteristics tissue: ovary pieces
developmental stage: vitellogenic
Growth protocol Females were sacrificed at different times during the annual reproductive cycle and pieces of the ovary were deep-frozen
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from vitellogenic and atretic ovaries using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions
Label Cy5
Label protocol Total RNA (0.5 μg) from each sample was amplified and labelled with fluorescent cyanine dyes, Cy3 or Cy5, using the Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems) following the manufacturer's instructions with minor modifications
 
Channel 2
Source name IR-At-2
Organism Solea senegalensis
Characteristics tissue: ovary pieces
developmental stage: atretic
Growth protocol Females were sacrificed at different times during the annual reproductive cycle and pieces of the ovary were deep-frozen
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from vitellogenic and atretic ovaries using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions
Label Cy3
Label protocol Total RNA (0.5 μg) from each sample was amplified and labelled with fluorescent cyanine dyes, Cy3 or Cy5, using the Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems) following the manufacturer's instructions with minor modifications
 
 
Hybridization protocol Hybridizations were carried out for 17 h at 60°C using Agilent's gaskets G2534-60002, G2534A hybridization chambers, and DNA Hybridization Oven G2545A, according to the manufacturer's instructions
Scan protocol Microarray raw data were obtained using Agilent's DNA Microarray Scanner G2505B and Feature Extraction software (v10.1)
Description Biological replicate 2 of 3
Data processing The raw fluorescence intensity data were processed using the Polyphemus™ software (Oryzon Genomics), Q-Splines normalization.
 
Submission date Jul 27, 2009
Last update date Oct 02, 2009
Contact name angela tingaud-sequeira
E-mail(s) angela.tingaud@u-bordeaux1.fr
Organization name Université Bordeaux 1
Lab GPP
Street address avenue des Facultés
City Talence
ZIP/Postal code 33400
Country France
 
Platform ID GPL8931
Series (2)
GSE17334 Oogenesis in Solea senegalensis: vitellogenic versus atretic ovaries
GSE17337 Oogenesis in Solea senegalensis: various developmental stages

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing Vt/At

Data table
ID_REF VALUE
CL859CONTIG1-ENSDARG00000019940 -0.177025
CL85CONTIG1 -0.159764
CL860CONTIG1 -0.2829
CL861CONTIG1-ENSDARG00000028012 0.466164
CL862CONTIG1 -0.27027
CL863CONTIG1-ENSDARG00000016576 -0.221932
CL864CONTIG1-ENSDARG00000015343 0.088134
CL865CONTIG1 0.007028
CL866CONTIG1 -0.069048
CL867CONTIG1-ENSDARG00000040251 0.160818
CL868CONTIG1 -0.211613
CL1100CONTIG1-ENSDARG00000007219 0.030037
CL869CONTIG1 -0.141702
CL86CONTIG1-ENSDARG00000029606 -0.188889
CL870CONTIG1 -0.734174
CL871CONTIG1-ENSDARG00000024278 -0.204262
CL872CONTIG1 -0.041793
CL873CONTIG1 -0.340153
CL874CONTIG1 -0.298122
CL876CONTIG1-ENSDARG00000015246 0.235925

Total number of rows: 3688

Table truncated, full table size 123 Kbytes.




Supplementary file Size Download File type/resource
GSM433593_IR-Vt-2_vs_IR-At-2-D1-H11-Raw.txt.gz 149.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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