|
| Status |
Public on Apr 21, 2010 |
| Title |
Lymph node metastasis MT-13 |
| Sample type |
RNA |
| |
|
| Source name |
Lymph node metastasis from patient with malignant cutaneous melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Fresh frozen lymph nodes
|
| Growth protocol |
Normal human melanocyte cultures were bough from PromoCell (Heidelberg, Germany). Melanoma cell lines were obtained from surgical melanoma samples and cultured in RPMI medium supplemented with 10% FCS, HEPES buffer, glutamine and antibiotics (Biowhittaker).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using mirVana miRNA Isolation Kit (Applied Biosystem/Ambion, Austin, TX) according to the protocol recommended by the manifacturer.
|
| Label |
Cy3
|
| Label protocol |
120 ng of total RNA were were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase. Labeled RNA was purified using Micro Bio Spin 6 Columns (Bio-Rad, 732-6221)
|
| |
|
| Hybridization protocol |
Labeled RNA was hybridized onto Agilent miRNA array (G4470A) for 18-20 hours at 55°C
|
| Scan protocol |
Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v1.0. Images obtained after scanning were processed with Feature Extraction Software 9.5.3.1 (Agilent, Santa Clara, CA)
|
| Description |
miRNA expression profile
|
| Data processing |
Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized, log transformed and median centered. Only normalized miRNAs with less than 20% missing values across the samples were included in the further analysis.
|
| |
|
| Submission date |
Dec 08, 2009 |
| Last update date |
Apr 21, 2010 |
| Contact name |
Stefano Caramuta |
| E-mail(s) |
[email protected]
|
| Organization name |
Karolinska Institutet
|
| Department |
Molecular Medicine and Surgery
|
| Lab |
Medical Genetics
|
| Street address |
CMM L8:01, Karolinska University Hospital
|
| City |
Stockholm |
| ZIP/Postal code |
17176 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL9081 |
| Series (1) |
| GSE19387 |
MicroRNA Expression Profiles Associated with Mutational Status and Survival in Malignant Melanoma |
|
