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Sample GSM1649090 Query DataSets for GSM1649090
Status Public on Mar 20, 2018
Title BCBL1_NaB_48hrs_rep1
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 NaB1
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

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
340381 0.225103127
340405 0.022668037
340453 0.168212779
340476 0.387926571
340548 -0.102168757
340382 -0.167772557
340430 0.195473468
340454 0.462222749
340477 0.27511607
340501 0.081176231
340525 -0.104819781
340549 -0.181540888
340407 0.521476375
340455 -0.1107357
340526 -0.028756828
340550 -0.047105999
340408 0.014196657
340432 0.613360898
340456 -0.08253455
340479 -0.523867981

Total number of rows: 12087

Table truncated, full table size 229 Kbytes.




Supplementary file Size Download File type/resource
GSM1649090_35026.gpr.gz 1.3 Mb (ftp)(http) GPR
GSM1649090_35026.txt.gz 2.4 Mb (ftp)(http) TXT
GSM1649090_35026_RG_geneavg_NaB1.txt.gz 665.9 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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