|
| Status |
Public on Mar 01, 2005 |
| Title |
Operon 2054M vs. 2056PT (ID407) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
primary HNSCC (oropharynx; grade 2) from a 49 year old male (sample 2056PT)
|
| Organism |
Homo sapiens |
| Extracted molecule |
total RNA |
| |
|
| Channel 2 |
| Source name |
lymph node metastasis of the same patient (2054M)
|
| Organism |
Homo sapiens |
| Extracted molecule |
total RNA |
| |
|
| |
| Description |
the tumor specimens contained > 80% tumor tissue and < 10% necrotic debris. 30-50 µg of frozen tissue sample were combined with 1 µl Trizol (Invitrogen) and dispersed using an Ultra-Turrax T25 tissue homogenizer (IKA). Total RNA was extracted according to the recommendations given by the Trizol protocol and further purified on RNeasy Mini spin columns (QIAGEN). aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs. Hybridization was carried out at 37 °C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).
Keywords = cancer
Keywords = HNSCC
Keywords = human
Keywords = spotted long oligonucleotide array
Keywords = oligo
Keywords = 70mer
Keywords = Operon
Keywords = comparative study
Keywords = statistics & numerical data
Keywords = sensitivity and specificity
|
| |
|
| Submission date |
Sep 01, 2004 |
| Last update date |
Oct 28, 2005 |
| Contact name |
Joerg Schlingemann |
| E-mail(s) |
[email protected]
|
| Phone |
+49 6221 424672
|
| Fax |
+49 6221 424639
|
| URL |
http://www.dkfz-heidelberg.de/kompl_genome/index.html
|
| Organization name |
German Cancer Research Center (DKFZ)
|
| Department |
Molecular Biology (B060)
|
| Lab |
Expression Profiling Facility
|
| Street address |
Technologiepark III, Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1384 |
| Series (1) |
| GSE1722 |
Cross-platform reproducibility of oligonucleotide microarray expression profiles |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
log2-transformed normalized expression ratio (Cy5/Cy3); spot replicates were averaged. Spots not recognized by the image analysis software "GenePix Pro 5.0" (Axon Instruments) were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002). To eliminate low quality data, the data points were ranked according to spot homogeneity, as assayed by the ratio of median to mean fluorescence intensity, the ratio of spot to local background intensity and the standard deviation of the log2 ratios between spot replicates. Those data points ranked among the lower 20% were removed from the data set. Genes that could not be quantified in more than 33% of all experiments of the experimental series after filtering were excluded as well. |
| CH1_RAW_SPOT1 |
Cy3 raw fluorescence intensity for spot replicate 1 |
| CH1_SD_SPOT1 |
standard deviation of Cy3 raw fluorescence intensity for spot replicate 1 |
| CH1_BKD_RAW_SPOT1 |
Cy3 raw fluorescence intensity for local background of spot replicate 1 |
| CH1_BKD_SD_SPOT1 |
standard deviation of Cy3 raw fluorescence intensity for local background of spot replicate 1 |
| CH2_RAW_SPOT1 |
Cy5 raw fluorescence intensity for spot replicate 1 |
| CH2_SD_SPOT1 |
standard deviation of Cy5 raw fluorescence intensity for spot replicate 1 |
| CH2_BKD_RAW_SPOT1 |
Cy5 raw fluorescence intensity for local background of spot replicate 1 |
| CH2_BKD_SD_SPOT1 |
standard deviation of Cy5 raw fluorescence intensity for local background of spot replicate 1 |
| FLAGS_SPOT1 |
GenePix flag for spot replicate 1 |
| CH1_RAW_SPOT2 |
Cy3 raw fluorescence intensity for spot replicate 2 |
| CH1_SD_SPOT2 |
standard deviation of Cy3 raw fluorescence intensity for spot replicate 2 |
| CH1_BKD_RAW_SPOT2 |
Cy3 raw fluorescence intensity for local background of spot replicate 2 |
| CH1_BKD_SD_SPOT2 |
standard deviation of Cy3 raw fluorescence intensity for local background of spot replicate 2 |
| CH2_RAW_SPOT2 |
Cy5 raw fluorescence intensity for spot replicate 2 |
| CH2_SD_SPOT2 |
standard deviation of Cy5 raw fluorescence intensity for spot replicate 2 |
| CH2_BKD_RAW_SPOT2 |
Cy5 raw fluorescence intensity for local background of spot replicate 2 |
| CH2_BKD_SD_SPOT2 |
standard deviation of Cy5 raw fluorescence intensity for local background of spot replicate 2 |
| FLAGS_SPOT2 |
GenePix flag for spot replicate 2 |
