|
| Status |
Public on Mar 18, 2008 |
| Title |
BL30 vs BL30 (B95-8) – RNA pair 2 (Dye Swap) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Epstein Barr virus infected Burkitt’s lymphoma cell line, BL30 (B95-8)
|
| Organism |
Homo sapiens |
| Characteristics |
BL30 (B95-8) RNA prep 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen total RNA purification kit – Standard conditions
|
| Label |
Cy3
|
| Label protocol |
Standard Agilent labeling protocol
|
| |
|
| Channel 2 |
| Source name |
Epstein Barr virus negative Burkitt's lymphoma cell line, BL30
|
| Organism |
Homo sapiens |
| Characteristics |
BL30 – RNA prep 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen total RNA purification kit – Standard conditions
|
| Label |
Cy5
|
| Label protocol |
Standard Agilent labeling protocol
|
| |
|
| |
| Hybridization protocol |
The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.
Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.
|
| Scan protocol |
Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).
|
| Description |
No additional description
|
| Data processing |
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).
|
| |
|
| Submission date |
Mar 14, 2008 |
| Last update date |
Mar 17, 2008 |
| Contact name |
Erik K Flemington |
| E-mail(s) |
eflemin@tulane.edu
|
| Phone |
504 988-1167
|
| Organization name |
Tulane Health Sciences Center
|
| Department |
Pathology
|
| Street address |
1430 Tulane Ave., SL79
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE10863 |
microRNA-155 is an Epstein-Barr Virus induced gene that modulates EBV-regulated gene expression (EBV infection) |
| GSE10868 |
microRNA-155 is an Epstein-Barr Virus induced gene that modulates Epstein Barr virus regulated gene expression pathways |
|
