|
| Status |
Public on Sep 14, 2010 |
| Title |
4390-8271-Cy5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
4390-8271
|
| Organism |
Homo sapiens |
| Characteristics |
sex: M
sample_type: sample
tumor_entity_subtype: pGBIV
ageatsampling: 66
overall.survival..days.: 417
chemotherapy: yes
radiation.therapy: yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were prepared from fresh frozen tumor tissue using ultracentrifugation [PMID: 12937144]
|
| Label |
Cy5
|
| Label protocol |
Samples were amplified and labeled using TAcKLE Protocol [PMID: 15718295]
|
| |
|
| Channel 2 |
| Source name |
8076-8077
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Universal Human Reference Total RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2ug universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000)
|
| Label |
Cy3
|
| Label protocol |
Samples were amplified and labeled using TAcKLE Protocol [PMID: 15718295]
|
| |
|
| |
| Hybridization protocol |
Purified and dye-labeled sample and reference cDNA (Human Reference RNA, Stratagene, LaJolla, USA) was pooled an mixed with 520 µl hybridisation buffer (4x SSC, 50perc formamide, 2perc SDS), agitated for 60 min at 60C, heated for 10 min at 70C on a thermo mixer and subsequently applied to preheated (60C) microarrays mounted in hybridisation chambers. Hybridisations were performed for 23 h at 42C and a rotation speed of 4 rpm in an Agilent DNA Microarray Hybridisation Oven (Agilent, Santa Clara, USA). The arrays were washed at 35C with (i) 0.5x SSC, 0.1perc SDS for 4 min; (ii) 0.05x SSC, 0.1perc SDS for 4 min; (iii) 0.05x SSC for 2 min; (iv) 0.05x SSC, 0.05perc Tween for 30 sec. Immediately thereafter, slides were dried by centrifugation in 50 ml Falcon tubes at 2500 rpm for 5 min.
|
| 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 |
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 variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002).
|
| |
|
| 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 |
GPL9190 |
| Series (1) |
| GSE18166 |
Genome-Wide Profiling of Astrocytic Gliomas |
|
