|
| Status |
Public on Aug 29, 2008 |
| Title |
deceased, 8903 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
breast cancer tumor, deceased patient
|
| Organism |
Homo sapiens |
| Characteristics |
fresh frozen tumour
estrogen receptor negative
progesterone receptor negative
aneuploid
comedo
breast preserving surgery
age at diagnosis: 38
tumour size: 18 mm
post surgical radio therapy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| 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 |
control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| 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 6.0.0.45 (Axon Instruments).
|
| Description |
lymph-node-negative breast cancer
|
| Data processing |
Intensities were calculated by median spot - median background. Flagged spots and spots for which background adjusted intensities were <0 or >65 000 were excluded 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. pin-based Lowess normalization were performed with 12 blocks in each group
|
| |
|
| Submission date |
Jul 10, 2008 |
| Last update date |
Jul 16, 2008 |
| Contact name |
Elin Karlsson |
| E-mail(s) |
elin.karlsson@gu.se
|
| Organization name |
Göteborg University
|
| Department |
Oncology
|
| Street address |
Blå stråket 2
|
| City |
Göteborg |
| ZIP/Postal code |
SE-41345 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL5186 |
| Series (1) |
| GSE12071 |
Gene expression variation to predict 10-year survival in lymph-node-negative breast cancer |
|
