|
| Status |
Public on Mar 21, 2013 |
| Title |
MDBK_InVitro_Rep1_DyeSwap2-1_2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
AlHV-1 infected MDBK cells
|
| Organism |
Bos taurus |
| Characteristics |
cell line: MDBK cells from ATCC (CCL-22)
infection: AlHV-1 C500 strain
|
| Growth protocol |
Madin-darby bovine kidney cells (MDBK, ATCC) were cultured in Dulbecco’s modified Essential Medium (DMEM, Life technologies) containing 10 % foetal calf serum (FCS, Bio Wittaker). The pathogenic AlHV-1 C500 strain isolated from an ox with MCF and the AlHV-1 BAC clone were used throughout this study . The virus strains were maintained by limited passage (<5).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA samples were obtained from cultured MDBK cells using the RNeasy miniprep kit with on-column DNAse I treatment (Qiagen). The absence of contaminating genomic viral DNA was determined by PCR on all RNA samples and RNA quality was tested on an Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy5
|
| Label protocol |
Samples were prepared with the standard RNA Gene Expression Agilent Kit (QuickAmp) which includes a poly-dT amplification and Cy3 or Cy5 labeling (cyanine) steps.
|
| |
|
| Channel 2 |
| Source name |
Mock infected MDBK cells
|
| Organism |
Bos taurus |
| Characteristics |
cell line: MDBK cells from ATCC (CCL-22)
infection: mock-infection
|
| Growth protocol |
Madin-darby bovine kidney cells (MDBK, ATCC) were cultured in Dulbecco’s modified Essential Medium (DMEM, Life technologies) containing 10 % foetal calf serum (FCS, Bio Wittaker). The pathogenic AlHV-1 C500 strain isolated from an ox with MCF and the AlHV-1 BAC clone were used throughout this study . The virus strains were maintained by limited passage (<5).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA samples were obtained from cultured MDBK cells using the RNeasy miniprep kit with on-column DNAse I treatment (Qiagen). The absence of contaminating genomic viral DNA was determined by PCR on all RNA samples and RNA quality was tested on an Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Samples were prepared with the standard RNA Gene Expression Agilent Kit (QuickAmp) which includes a poly-dT amplification and Cy3 or Cy5 labeling (cyanine) steps.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed according to the VIB Leuven Microarray facility's standard protocol: hybridization was carried out at 65°C for 17 hours at 10 rpm, after 17 h the glass slides were washed without triton.
|
| Scan protocol |
After hybridization, the glass slides were dried and scanned using a Scanner G2505C (Agilent Technologies, USA, VIB Leuven Microarray facility).
|
| Data processing |
The data was analyzed in R using the 'limma' package from the Bioconductor project. The two-colour arrays were first background corrected with the 'norm exp' method and an offset of 50 and then normalized with a 'loess' normalization.
|
| |
|
| Submission date |
Sep 05, 2012 |
| Last update date |
Mar 21, 2013 |
| Contact name |
Leonor Palmeira |
| Organization name |
University of Liege
|
| Department |
Faculty of Veterinary Medicine
|
| Lab |
Immunology-Vaccinology
|
| Street address |
Bd Colonster 20
|
| City |
Liege |
| ZIP/Postal code |
4000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL16018 |
| Series (1) |
| GSE40644 |
Transcriptional analysis of Bos taurus and AlHV-1 in MDBK infected cells and in lymph nodes of infected calves |
|
