|
| Status |
Public on Jan 20, 2015 |
| Title |
TC006 |
| Sample type |
RNA |
| |
|
| Source name |
Fresh frozen biopsy from primary papillary thyroid tumors
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: papillary thyroid carcinoma patient
gender: male
tumor stage: T3-T4
age: ≥45
|
| Treatment protocol |
Fresh frozen tumor biopsy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cell pellets was isolated with Rneasy Mini Kit (Qiagen), following the manufacterer's instructon. A fraction was quantitated by spectrophotometric measure using NanoDrop. RNA integrity was evaluated in agarose gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
cRNA synthesis was made using 3`IVT Express kit (Affymetrix) following manufacterer's instructions and starting with 150ng of total RNA
|
| |
|
| Hybridization protocol |
Labeled cRNA was fragmented in fragmentation buffer (5x buffer:200 mM Tris-acetate (pH 8.1)/500nM KOAc/150 mM MgOAc) before hybridization on the array. Fragmented cRNA was hybridized to the nicroarrays in 90ul hybridization solution. GeneTitan Hybridization, Wash and Stain kit for 3`IVT arrays (Affymetrix) was used for preparing hybridization mixes and processing plate array in GeneTitan
|
| Scan protocol |
Human Genome U219 array plate was processed in GeneTitan according to manufacturer's instructions
|
| Description |
A1369-06
|
| Data processing |
The data were analyzed with RMA method in R
|
| |
|
| Submission date |
Jan 18, 2015 |
| Last update date |
Jan 20, 2015 |
| Contact name |
Jan Alsner |
| E-mail(s) |
jan@oncology.au.dk
|
| Organization name |
Aarhus University Hospital
|
| Department |
Experimental clinical Oncology
|
| Street address |
Nørrebrogade 44, Bldg. 5
|
| City |
Aarhus C |
| ZIP/Postal code |
8000 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE65074 |
Gene expression classifier in papillary thyroid carcinoma: validation and application of a classifier for prognostication |
|
