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Sample GSM311974 Query DataSets for GSM311974
Status Public on Aug 12, 2008
Title 1047LB
Sample type RNA
 
Channel 1
Source name serous ovarian adenocarcinoma
Organism Homo sapiens
Characteristics fresh frozen tumour
5 year survivor
stage IIIab
macroscopic residual tumor
age at diagnosis 44
post surgical chemo therapy farmorubicine, carboplatin and cyclophosphamide
Extracted molecule total RNA
Extraction protocol Homogenization with Trizol followed by total RNA extraction with Rneasy mini kit following manufacturer's instructions (Qiagen).
Label Cy3
Label protocol Probes labelled with Cy3 were synthesized from 5 µg of the total tumour RNA and reference labelled with Cy5 were synthesized from 5 µg of commercial reference RNA by reverse transcription.
 
Channel 2
Source name Universal Human Reference RNA purchased from Stratagene
Organism Homo sapiens
Characteristics Reference
Extracted molecule total RNA
Extraction protocol Homogenization with Trizol followed by total RNA extraction with Rneasy mini kit following manufacturer's instructions (Qiagen).
Label Cy5
Label protocol Probes labelled with Cy3 were synthesized from 5 µg of the total tumour RNA and reference labelled with Cy5 were synthesized from 5 µg of commercial reference RNA by reverse transcription.
 
 
Hybridization protocol The probes were purified using ChipShot™ labelling cleanup system (Promega). The hybridizations were carried out using Pronto! Micro Array reagent systems (Corning Inc.). For each sample, labelled tumour cDNA and reference cDNA were co-precipitated and hybridised to the oligoarray slide. After hybridization, slides were washed sequential.
Scan protocol Scanned on an Agilent G2565AA scanner.
Images were quantified using Genepix 6.0.0.74 (Axon Instruments).
Description Comparison of ovarian tumors of 5 year survivors to deceased patients
Data processing Intensities were calculated by mean spot - median background. Flagged spots were removed as well as spots with intensities below 20 in both channels. Intensities below 20 in one channel were set to 20 to compensate for extreme quotients. Loess normalization was used
 
Submission date Aug 12, 2008
Last update date Aug 13, 2008
Contact name Karolina Partheen
E-mail(s) karolina.partheen@gu.se
Phone +46+31 342 78 55
Fax +46 +31 41 72 05
Organization name University of Gothenburg
Department department of Oncology
Street address Blå Stråket 2
City Gothenburg
ZIP/Postal code 413 45
Country Sweden
 
Platform ID GPL5886
Series (1)
GSE12418 Stage III serous ovarian adenocarcinomas

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

Data table
ID_REF VALUE
1 -1.197937072
2 -1.288387634
3 null
4 null
5 null
6 null
7 null
8 null
9 0.437703105
10 null
11 null
12 null
13 null
14 null
15 null
16 null
17 null
18 null
19 null
20 null

Total number of rows: 30000

Table truncated, full table size 425 Kbytes.




Supplementary file Size Download File type/resource
GSM311974.gpr.gz 2.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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