|
| Status |
Public on Aug 12, 2008 |
| Title |
123DC |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
serous ovarian adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
fresh frozen tumour
deceased
stage IIIc
macroscopic residual tumor
age at diagnosis 56
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) |
[email protected]
|
| 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 |
|
