|
| Status |
Public on Apr 01, 2017 |
| Title |
Patient 1 - Pre-treatment Biopsy - Day 1 - mAdbID:120025 |
| Sample type |
RNA |
| |
|
| Source name |
Pre-treatment Biopsy - Day 1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
disease state: metastatic melanoma
day: 1
|
| Treatment protocol |
Treatment time: day 1
In-vivo treatment: Biopsies (incisional, excisional, or core biopsies, and fine needle aspiration biopsies) of cutaneous metastatic melanoma were obtained on day 1 (baseline, no treatment).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample Extraction Protocol
Other: Cells from melanoma metastasis were lysed directly in QIAzol Lysis Reagent (Qiagen, Hilden, Germany) and RNA was extracted according to the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Affymetrix Labeling Protocol
Other: RNA was amplified using the Ambion WT expression kit (Life Technologies, Carlsbad, CA). Fragmented single-stranded sense DNA were terminally labeled with biotin according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Affymetrix Hybridization Protocol
Other: Fragmented single-stranded sense DNA were hybridized to the Human GeneChip 1.0 ST array and stained on a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.
|
| Scan protocol |
Scanning Protocol
Other: Arrays were scanned on a GeneChip Scanner 3000-7G (Affymetrix).
|
| Description |
mAdb experiment ID: 120025
|
| Data processing |
Data Processing Protocol
Calculation Method: Data were analyzed using Expression Console and Transcriptome Analysis Console Software. After Robust Multichip Average normalization, differentially expressed genes were identified by paired test with a significance cut off p <= 0.05 and fold change (linear) of < -2 or > 2 (Affymetrix).
|
| |
|
| Submission date |
Apr 07, 2016 |
| Last update date |
Apr 01, 2017 |
| Contact name |
Francesco Maria Marincola |
| E-mail(s) |
fmarincola@sidra.org
|
| Phone |
301-793-8210
|
| Organization name |
Sidra Medical and Research Center
|
| Street address |
Al Nasr Tower, AL Corniche Street, PO Box 26999
|
| City |
Doha |
| ZIP/Postal code |
PO Box 26999 |
| Country |
Qatar |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE80028 |
Vaccination and topical imiquimod treatment promote immune signatures in melanoma |
|
