|
| Status |
Public on Mar 20, 2018 |
| Title |
BCBL1_NaB_48hrs_rep3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
BCBL-1 untreated 48hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BCBL-1
cell type: latently infected KSHV body cavity-based, lymphoma-derived cell line
treated with: none (untreated control)
|
| Treatment protocol |
BCBL-1 cells were left untreated or treated for 48 hours with 1:20 P. gingivalis spent media, 0.3 mM NaB, or 0.25 ng/mL TPA.
|
| Growth protocol |
BCBL-1, a latently infected KSHV body cavity-based, lymphoma-derived cell line, were maintained in 5% CO2 at 37°C in RPMI 1640 medium supplemented with 10% FBS containing penicillin, streptomycin, sodium pyruvate, and L-glutamine (GIBCO-BRL, Gaithersburg, MD).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from BCBL-1 cells that were either untreated or treated with NaB, TPA, or spent medium from P. gingivalis using the RNeasy kit from Qiagen (Valencia, CA). Any DNA contamination was then removed from the RNA using the DNAfree kit from Ambion, and the RNA was concentrated.
|
| Label |
Cy3
|
| Label protocol |
cDNA was synthesized using Reverse transcriptase PCR with Taq polymerase (Roche) and N6 primers. Primers annealed at 50°C, followed by 35 cycles of 94°C for 45 seconds, 50°C for 45 seconds, 75°C for 4 seconds, plus 2 seconds for each cycle. Cy3 and Cy5 dyes were incorporated into the control and treatment samples, respectively.
|
| |
|
| Channel 2 |
| Source name |
BCBL-1 NaB 48hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BCBL-1
cell type: latently infected KSHV body cavity-based, lymphoma-derived cell line
treated with: 0.3 mM NaB for 48 hrs
|
| Treatment protocol |
BCBL-1 cells were left untreated or treated for 48 hours with 1:20 P. gingivalis spent media, 0.3 mM NaB, or 0.25 ng/mL TPA.
|
| Growth protocol |
BCBL-1, a latently infected KSHV body cavity-based, lymphoma-derived cell line, were maintained in 5% CO2 at 37°C in RPMI 1640 medium supplemented with 10% FBS containing penicillin, streptomycin, sodium pyruvate, and L-glutamine (GIBCO-BRL, Gaithersburg, MD).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from BCBL-1 cells that were either untreated or treated with NaB, TPA, or spent medium from P. gingivalis using the RNeasy kit from Qiagen (Valencia, CA). Any DNA contamination was then removed from the RNA using the DNAfree kit from Ambion, and the RNA was concentrated.
|
| Label |
Cy5
|
| Label protocol |
cDNA was synthesized using Reverse transcriptase PCR with Taq polymerase (Roche) and N6 primers. Primers annealed at 50°C, followed by 35 cycles of 94°C for 45 seconds, 50°C for 45 seconds, 75°C for 4 seconds, plus 2 seconds for each cycle. Cy3 and Cy5 dyes were incorporated into the control and treatment samples, respectively.
|
| |
|
| |
| Hybridization protocol |
Samples were applied to array in a hybridization chamber and placed at 65°C overnight. Coverslips were removed with 2X SSC with 0.25% SDS, washed once in 1X SSC for 3-5 min, then washed twice in 0.2X SSC for 3-5 min at 50-65°C. Slides were spun at 500 rpm for 4 min.
|
| Scan protocol |
Microarrays were scanned and gridded with GenePix 3.0 (Axon Corp.)
|
| Description |
NaB3
|
| Data processing |
The limma package from Bioconductor was used. background subtracted using normexp, normalized using print-tip loess and G-quantiles normalization. M values were calculated as the log2 of the spot intensity for the sample treated with a viral replication inducer over the spot intensity of the untreated sample and spots representing the same gene were averaged.
|
| |
|
| Submission date |
Apr 02, 2015 |
| Last update date |
Mar 20, 2018 |
| Contact name |
Jennifer Webster-Cyriaque |
| E-mail(s) |
Jennifer_Cyriaque@unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Dental Research
|
| Street address |
385 S. Columbia St.
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7455 |
| Country |
USA |
| |
|
| Platform ID |
GPL19981 |
| Series (1) |
| GSE67532 |
Kaposi’s Sarcoma-associated Herpesvirus Reactivation by Bacteria Promotes the Hypoxia Response and Epigenetic Regulation |
|
