|
| Status |
Public on Oct 18, 2007 |
| Title |
FEC100_0141_A |
| Sample type |
RNA |
| |
|
| Source name |
FEC100_0141_A Breast tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
Breast tumor tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All RNA was prepared on the same platform by the CsCl-cushion, as described (Chirgwin, 1979, Biochemistry, 18, 5294-5299.). The quality and the quantity of RNA samples were evaluated by Agilent 2100 Bioanalyser RNA LabChip kit (Agilent Technologies, Palo Alto, CA, USA).
|
| Label |
33P
|
| Label protocol |
Between 0.4 and one µg of total RNA was used as template to generate cDNA bearing T7 promoter, then antisense RNA (aRNA) was generated by in vitro transcription using MEGAscript technology according to the Ambion protocol (Ambion Inc., Austin TX). An aliquot of 2µg of labelled aRNA was then primed with random hexaprimers and reverse transcribed with a mix of cold dNTPs and [a-33P]dCTP.
|
| |
|
| Hybridization protocol |
Labelled cDNAs were then hybridized in 0.3 ml hybridization mix in scintillation vials for 48 h at 68° C. After hybridization filters were washed twice in 0.1x SSC, 0.1% SDS at 68° C for 90 min.
|
| Scan protocol |
DNA microarrays were scanned at 25-µm resolution using a Fuji BAS 5000 image plate system (Raytest, Paris, France). The hybridization signals were quantified using ArrayGauge software v.1.3 (Fuji, Ltd, Tokyo, Japan).
|
| Description |
Patients included in clinical trials (PACS01 / PEGASE01).
|
| Data processing |
Data were background noise subtracted (negative controls ± 6 SD), then normalized by original global intensity of hybridization and finally log2-transformed. Only genes well measured for 70% of patients were retained. Data have been normalized with an expression data correction by the amount of PCR product spotted onto the membrane (ratio : Patient probe / Testing probe).
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| |
|
| Submission date |
Feb 12, 2007 |
| Last update date |
Oct 18, 2007 |
| Contact name |
Wilfried Gouraud |
| Organization name |
ICO - UMGC
|
| Department |
Integrated Center of Oncology René Gauducheau
|
| Lab |
Omics Data Science Unit
|
| Street address |
bd Jacques Monod
|
| City |
Saint Herblain |
| ZIP/Postal code |
44805 |
| Country |
France |
| |
|
| Platform ID |
GPL4819 |
| Series (1) |
| GSE7017 |
Establishment of a predictive clinicogenomic model for FEC100 regimen in node-positive breast cancer patients |
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