|
| Status |
Public on Oct 30, 2008 |
| Title |
patient_4_a |
| Sample type |
RNA |
| |
|
| Source name |
melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
punch biopsy
in-transit disease
M_stage_IIIB
Braf-WT_Nras-WT
|
| Treatment protocol |
Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
|
| Label |
biotin
|
| Label protocol |
one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
|
| |
|
| Hybridization protocol |
labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
|
| Scan protocol |
Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
|
| Description |
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
| Data processing |
Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
|
| |
|
| Submission date |
Jan 25, 2008 |
| Last update date |
Jan 25, 2008 |
| Contact name |
Christina Augustine |
| E-mail(s) |
christi.augustine@duke.edu
|
| Organization name |
Duke University Medical Center
|
| Department |
Surgery
|
| Street address |
VAMC RmE4001 508 Fulton St.
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27705 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE10282 |
In-transit extremity melanoma I |
|
