|
| Status |
Public on Sep 14, 2010 |
| Title |
4257-922-Cy3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
4209-873
|
| Organism |
Homo sapiens |
| Characteristics |
sex: Pooled
sample_type: control
tumor_entity_subtype: NA
ageatsampling: NA
overall.survival..days.: NA
chemotherapy: NA
radiation.therapy: NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction from peripheral blood leukocytes was performed according to standard protocol
|
| Label |
Cy5
|
| Label protocol |
Cy3-/ Cy5-conjugated dCTP by use of BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany)
|
| |
|
| Channel 2 |
| Source name |
4257-922
|
| Organism |
Homo sapiens |
| Characteristics |
sex: M
sample_type: sample
tumor_entity_subtype: AII
ageatsampling: 41
overall.survival..days.: NA
chemotherapy: no data
radiation.therapy: no data
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were prepared from fresh frozen tumor tissue using ultracentrifugation [PMID: 12937144]
|
| Label |
Cy3
|
| Label protocol |
Cy3-/ Cy5-conjugated dCTP by use of BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany)
|
| |
|
| |
| Hybridization protocol |
Ten micrograms of tumor and reference DNA were combined with 300 mg of human Cot-1 DNA (Roche Diagnostics, Mannheim, Germany) and suspended in 125 ml of UltrahybTM hybridization buffer (Ambion, Bad Soden, Germany). Denaturation of combined DNA was performed at 75C for 10 min, followed by preannealing at 37C for 30 min. Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 hr at 37C.
|
| Scan protocol |
Hybridized microarrays were scanned at 5 µm resolution in a two-color Agilent Scanner G25505B (Agilent, Santa Clara, USA) with automatically adjusted PMT voltages according to manufacturer’s specification. Array raw data were generated from scanned images using Axon GenePixPro Software (v6.1.0.2)
|
| Description |
N/A
|
| Data processing |
Spot replicates were averaged. Spots not recognized by the image analysis software, or not passing the quality criteria were excluded from the calculations. Raw fluorescence intensities were normalized applying the printtip loess normalization function of limma.
|
| |
|
| Submission date |
Sep 18, 2009 |
| Last update date |
Sep 21, 2009 |
| Contact name |
Grischa Toedt |
| Organization name |
German Cancer Research Center (DKFZ)
|
| Department |
Molecular Genetics (B060)
|
| Lab |
Prof. Peter Lichter
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9189 |
| Series (1) |
| GSE18166 |
Genome-Wide Profiling of Astrocytic Gliomas |
|
