|
| Status |
Public on Dec 31, 2011 |
| Title |
L591 vs KMH2 rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Cell line KMH2 - Not EBV infected
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KMH2
infection: Not EBV infected
|
| Treatment protocol |
Not treated cells
|
| Growth protocol |
Cells were grown in RPMI medium supplemented with 10% Fetal Bovine Serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
cRNA was labeled usind Quick-Amp labeling kit (Agilent, USA, cat # 5190-0424). Briefly 250 ng of total RNA plus RNAs spikes (Spike A-cy3 or Spike B-cy5) and were primed with T7 DNA primer at 70°C for 10 min, then the first and second cDNA molecules were synthesized at 42°C for 2 h in the presence of RTase. The cRNA were made by T7 RNA polymerase plus rNTPs mixture and UTP labeled CY3 or Cy5.
|
| |
|
| Channel 2 |
| Source name |
Cell line L591- EBV infected
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: L591
infection: EBV infected
|
| Treatment protocol |
Not treated cells
|
| Growth protocol |
Cells were grown in RPMI medium supplemented with 10% Fetal Bovine Serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
cRNA was labeled usind Quick-Amp labeling kit (Agilent, USA, cat # 5190-0424). Briefly 250 ng of total RNA plus RNAs spikes (Spike A-cy3 or Spike B-cy5) and were primed with T7 DNA primer at 70°C for 10 min, then the first and second cDNA molecules were synthesized at 42°C for 2 h in the presence of RTase. The cRNA were made by T7 RNA polymerase plus rNTPs mixture and UTP labeled CY3 or Cy5.
|
| |
|
| |
| Hybridization protocol |
Oligoarray, 850 ng of each cy3 and cy5 labeled cRNA were fragmented at 60°C for 10 min, then equal volume of Agilent Hybridization buffer (50 ul) was added and hybridized using Agilent hybridization chambers at 65°C for 17 hours in an rotatory oven. After hybridization, slides were washed sequentially using 50 ml Falcon tubes; Agilent buffer1 for 1 minute; Agilent buffer 2 at 37°C for 1 min; Acetoniltrile for 10 seconds; Agilent stabilization and drying solution for 30 seconds.
|
| Scan protocol |
Scanned on an Agilent G2565BA scanner.
|
| Description |
Cells untreated, harvested after several passages.
|
| Data processing |
Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Apr 29, 2010 |
| Last update date |
Dec 31, 2011 |
| Contact name |
Renato David Puga |
| Organization name |
Universidade de São Paulo
|
| Department |
Instituto de Psiquiatria
|
| Lab |
Laboratório de Genética
|
| Street address |
Dr Ovidio Pires de Campos,785
|
| City |
São Paulo |
| State/province |
São Paulo |
| ZIP/Postal code |
05403-010 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE21586 |
Gene expression profile of classical Hodgkin lymphoma according to Epstein-Barr infection status |
|
