|
| Status |
Public on Sep 19, 2013 |
| Title |
Brain Metastasis 7 |
| Sample type |
RNA |
| |
|
| Source name |
Melanoma brain metastasis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain metastasis
disease: melanoma
clinical stage: IV
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
Cell lines were grown at 37C in a 5% CO2 humidified atmosphere, in RPMI 1640 supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from melanoma-related specimens by using the miRNeasy Mini Kit (QIAGEN) including an on-column DNase digestion step following the protocol provided by the manufacturer. RNA concentration was quantified using the Quant-iT™ RiboGreen® RNA assay kit (Invitrogen). The quality of the RNA was assessed by RNA Integrity Number (RIN) score on the Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized with Human Exon 1.0 ST Arrays (Affymetrix).
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instructions (Affymetrix).
|
| Description |
MBM-7
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array
|
| Data processing |
Data were analyzed in Expression Console 1.1 software (Affymetrix) using the core transcript set and employing the robust multi-array average algorithm (RMA) for background correction and normalization of data.
Core exons; genome build hg18.
|
| |
|
| Submission date |
Feb 25, 2013 |
| Last update date |
Sep 19, 2013 |
| Contact name |
Dave S.B. Hoon |
| E-mail(s) |
hoond@jwci.org
|
| Organization name |
Saint John's Cancer Institute
|
| Department |
Translational Molecular Medicine
|
| Street address |
2200 Santa Monica Boulevard
|
| City |
Santa Monica |
| State/province |
CA |
| ZIP/Postal code |
90403 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE44660 |
Affymetrix expression array data for melanoma progression to the brain |
| GSE44662 |
Genome-wide DNA methylation, gene expression, and copy number integrative analysis of melanoma brain metastasis |
|
