|
| Status |
Public on Mar 11, 2009 |
| Title |
Adenocarcinoma, bone marrow negative AC 12 |
| Sample type |
RNA |
| |
|
| Source name |
Human pulmonary adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
female pulmonary adenocarcinoma
bone marrow negative
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy Micro Kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle protocol from 50 ng total RNA
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on hgu133plus2 Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Post Hyb Wash No.1: 10 cycles of of 2 mixes/cycle with Wash Buffer A at 25°C. Post Hyb Wash No.2: 4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C. Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C. Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C. 2nd Stain: Stain the probe array for 10 minutes in antibody solution at 25°C. 3rd Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C. Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C. Hybridization Buffer: 100 mM MES 1 M [Na+] 20 mM EDTA 0.01% Tween 20. Wash Buffer A (Nonstringent): 6x SSPE 0.01% Tween 20. Wash Buffer B (Stringent): 100 mM MES 0.1 M [Na+] 0.01% Tween 20. Stain Buffer: 100 mM MES 1 M [Na+] 0.05% Tween 20. SAPE Solution: 100 mM MES 1 M [Na+] 0.05% Tween 20 2 mg/ml acetylated BSA 10 μg/ml Streptavidin Phycoerythrin. Antibody Solution: 100 mM MES 1 M [Na+] 0.05% Tween 20 2 mg/ml acetylated BSA 0.1 mg/ml Normal Goat IgG 3 μg/ml biotinylated Anti-Streptavidin.
|
| Scan protocol |
Affymetrix GeneChip Scanner 7G Pixel Size: 1.56 μ Filter: 570 nm Number of Scans: 1 Affymetrix GeneChip Operating Software 1.3
|
| Description |
Gene expression profile of lung tumor
|
| Data processing |
Data preprocessing using the GC Robust Multi-array Average (GC-RMA) method. Signal scaling against the median probe signal of three normal patients and log2-transformation. Genes for which information about the physical location is not given in the Affymetrix annotations files or is ambiguous are removed.
|
| |
|
| Submission date |
Mar 12, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Thomas Streichert |
| Organization name |
University Medical Center Hamburg-Eppendorf
|
| Department |
Institute For Clinical Chemistry / Central Laboratories
|
| Street address |
Martinistr. 52, Campus Forschung N27, 2. OG
|
| City |
Hamburg |
| ZIP/Postal code |
D-20246 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE10799 |
Gene expression profile of lung tumors |
|
| Relations |
| Reanalyzed by |
GSE60486 |
| Reanalyzed by |
GSE119087 |
