|
| Status |
Public on Jul 01, 2012 |
| Title |
patient 22 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
thyroid tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Oncocytic tumor
individual: patient 22
|
| Treatment protocol |
Human tumoral and paired control tissues.
|
| Growth protocol |
Human thyroid tissues.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA were extracted using a trizol® Reagent extraction procedure. RNA quality was checked on a bionalyzer and considered when RIN> 8
|
| Label |
cy3
|
| Label protocol |
The Cy3 (test) and Cy5 (reference) label were performed using the Amino Allyl MessageAmp™ II CyDye™ aRNA Amplification kit (Ambion, Cambridgeshire, UK) and the RNA fragmentation Reagents kit (Ambion).
|
| |
|
| Channel 2 |
| Source name |
normal thyroid tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pool of paired control normal thyroid tissue
|
| Treatment protocol |
Human tumoral and paired control tissues.
|
| Growth protocol |
Human thyroid tissues.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA were extracted using a trizol® Reagent extraction procedure. RNA quality was checked on a bionalyzer and considered when RIN> 8
|
| Label |
cy5
|
| Label protocol |
The Cy3 (test) and Cy5 (reference) label were performed using the Amino Allyl MessageAmp™ II CyDye™ aRNA Amplification kit (Ambion, Cambridgeshire, UK) and the RNA fragmentation Reagents kit (Ambion).
|
| |
|
| |
| Hybridization protocol |
The microarrays were first incubated at 50°C in a 50mM Ethanolamine - 100mM Tris base – SDS 0.1% solution for 15 minutes, and in a SSC 4x – 0.1% SDS solution for 15 minutes. The microarrays were then pre-hybridized 1 hour at 42°C. For each test, 20 µg of Cy3 labelled fragmented and hybridization mix resuspended samples were mixed with 20 µg of Cy5 labelled fragmented and hybridization mix resuspended reference. These mixes were denatured 2 minutes at 100°C and incubated 10 minutes at 37°C before hybridization. The microarrays were hybridized overnight at 42°C.
|
| Scan protocol |
The microarrays were scanned at 10 µM /pixel resolution with the Perkin Scanner (Waltham, MS, USA).
|
| Description |
paired control tissue
|
| Data processing |
The signal intensities were extracted with the Genepix Pro 5.1 image_analysis software (Axon Instruments, Sunnyvale, CA).
The Genespring GX software (version 7) was used to analyse the microarrays data. We first applied a “per spot and per chip” lowess normalisation on the data, normalising each chip to the median of the spots (50th percentile) and each gene to the median of the replicates (cut off in raw signal = 50).
|
| |
|
| Submission date |
Apr 03, 2012 |
| Last update date |
Jul 01, 2012 |
| Contact name |
frederique savagner |
| E-mail(s) |
frederique.savagner@univ-angers.fr
|
| Phone |
+33241353314
|
| Fax |
+33241354017
|
| Organization name |
Inserm
|
| Department |
U694
|
| Street address |
4 rue larrey
|
| City |
angers |
| ZIP/Postal code |
49033 |
| Country |
France |
| |
|
| Platform ID |
GPL15406 |
| Series (1) |
| GSE37017 |
Exploration of genes expression with a DNA microarray Cancerochip. |
|
