|
| Status |
Public on Sep 19, 2013 |
| Title |
Genomic DNA from lymph node metastasis 4 |
| Sample type |
genomic |
| |
|
| Source name |
Melanoma lymph node metastasis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: melanoma lymph node metastasis
disease: melanoma
clinical stage: III
|
| Growth protocol |
Cell lines were grown at 37C in a 5% CO2 humidified atmosphere, in RPMI 1640 (Life Technologies-Bethesda Research Laboratories) supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted from cell lines via the Qiagen DNeasy Kit according to standard instructions and from tissue after microdissection from 10 μm-thick paraffin-embedded archival tissue using Qiagen DNeasy Kit according to standard instructions.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol, run at USC core services.
|
| |
|
| Hybridization protocol |
Sodium bisulfite modification (SBM) was performed on 1µg of gDNA using the Zymo EZ DNA methylation kit (Zymo Research). An aliquot of SBM-gDNA was analyzed by MethyLight-based quality control to test bisulfite completeness. After correction of SBM-gDNA amount, 200 ng of SBM-gDNA was whole-genome amplified and enzymatically fragmented. Finally, the gDNA was hybridized to Infinium Human Methylation 450K BeadChips.
|
| Scan protocol |
The chips were scanned with Illumina iScan using the manufacturer's recommended settings.
|
| Description |
LNM-4
Melanoma lymph node metastasis-4
Cell line derived from patient.
|
| Data processing |
Data was extracted using the R package methylumi on Bioconductor.
|
| |
|
| Submission date |
Feb 25, 2013 |
| Last update date |
Dec 06, 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 |
GPL13534 |
| Series (2) |
| GSE44661 |
DNA methylation analysis of melanoma progression to brain metastasis |
| GSE44662 |
Genome-wide DNA methylation, gene expression, and copy number integrative analysis of melanoma brain metastasis |
|
