|
| Status |
Public on Apr 01, 2006 |
| Title |
1T |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Testicular DLBCL 1T
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: Testicular diffuse large B cell lymphoma
Sample origin: whole frozen tissue sections
Sample type: RNA
Amplification: linear, one-round
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and submitted to one round of linear amplification. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
|
| Label |
Cy5 or Cy3 (dye-reversal)
|
| Label protocol |
Cy3 or Cy5 molecules were directly incorporated during a cDNA synthesis reaction using amplified cRNA as starting material. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
|
| |
|
| Channel 2 |
| Source name |
Reference tonsil mix
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: 5 hyperplastic tonsils
Sample origin: whole frozen tissue sections
Sample type: RNA
Amplification: linear, one-round
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and submitted to one round of linear amplification. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
|
| Label |
Cy5 or Cy3 (dye-reversal)
|
| Label protocol |
Cy3 or Cy5 molecules were directly incorporated during a cDNA synthesis reaction using amplified cRNA as starting material. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
|
| |
|
| |
| Hybridization protocol |
Each hybridization was repeated as a dye reversal. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
|
| Scan protocol |
Fluorescent signals were extracted from the arrays by a DNA Microarray Scanner (Agilent, Palo Alto, California) and quantified using Imagene 5.5 software (Biodiscovery, El Segundo, California).
|
| Description |
A mix of 5 hyperplastic tonsils was used as a common reference. Each hybridization was repeated as a dye-reversal.
|
| Data processing |
Data were normalized and corrected for various biases according to Yang et al (PMID: 11842121). Ratios of expression in DLBCL (sample) compared to tonsil (reference) were calculated; weighted averages of dye-reversal experiments and confidence levels were calculated according to the Rosetta error model (Hughes et al, PMID: 10929718). Based on MA plots and the results from the error model, spots with an average intensity measurement A (0.5 log2 (Cy3Cy5)) lower than 7 over all experiments were excluded from further analysis.
|
| |
|
| Submission date |
Feb 01, 2006 |
| Last update date |
Feb 27, 2006 |
| Contact name |
Marije Booman |
| E-mail(s) |
[email protected]
|
| Organization name |
University Medical Center Groningen
|
| Department |
Pathology
|
| Street address |
P.O. Box 30001
|
| City |
Groningen |
| ZIP/Postal code |
9700 RB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL3408 |
| Series (2) |
| GSE4157 |
Gene expression analysis of immune privileged site-associated DLBCL: The effect of HLA class II downregulation |
| GSE4296 |
Gene expression analysis of testicular DLBCL: ABC or GCB subtype? |
|
