NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM433596 Query DataSets for GSM433596
Status Public on Oct 02, 2009
Title IR-Mt/At-2
Sample type RNA
 
Channel 1
Source name IR-Mt-2
Organism Solea senegalensis
Characteristics tissue: ovary pieces
developmental stage: mature
Treatment protocol To collect females with maturing and mature ovaries, fish were treated with intramuscular injection of 5 μg/kg GnRHa and killed 24-48 h later.
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 mature 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
Treatment protocol To collect females with maturing and mature ovaries, fish were treated with intramuscular injection of 5 μg/kg GnRHa and killed 24-48 h later.
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 mature 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)
GSE17335 Oogenesis in Solea senegalensis: mature versus atretic ovaries
GSE17337 Oogenesis in Solea senegalensis: various developmental stages

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

Data table
ID_REF VALUE
CL859CONTIG1-ENSDARG00000019940 -0.028363
CL85CONTIG1 -0.059962
CL860CONTIG1 -0.799813
CL861CONTIG1-ENSDARG00000028012 -0.164582
CL862CONTIG1 -0.045257
CL863CONTIG1-ENSDARG00000016576 -0.257069
CL864CONTIG1-ENSDARG00000015343 -0.283759
CL865CONTIG1 -0.355741
CL866CONTIG1 -0.002362
CL867CONTIG1-ENSDARG00000040251 0.082637
CL868CONTIG1 -0.224036
CL1100CONTIG1-ENSDARG00000007219 0.061926
CL869CONTIG1 -0.282092
CL86CONTIG1-ENSDARG00000029606 0.007238
CL870CONTIG1 -1.092184
CL871CONTIG1-ENSDARG00000024278 0.007394
CL872CONTIG1 -0.175197
CL873CONTIG1 -0.742834
CL874CONTIG1 -0.290254
CL876CONTIG1-ENSDARG00000015246 -0.150072

Total number of rows: 3688

Table truncated, full table size 123 Kbytes.




Supplementary file Size Download File type/resource
GSM433596_IR-Mt-2_vs_IR-At-2-D1-H8-Raw.txt.gz 149.6 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap