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Sample GSM838989 Query DataSets for GSM838989
Status Public on Apr 27, 2012
Title RBm11_SIVnegative_PBMCs
Sample type RNA
 
Source name SIV negative Rhesus macaque PBMCs
Organism Macaca mulatta
Characteristics disease state: SIV negative
tissue: PBMCs
Treatment protocol Rhesus macaques were infected intravenously with 200 TCID50 of SIVmac251 strain. The SIV-negative animals used here were sacrificed due to neurological and mental problems but were checked to ensure no history of bowel problems.
Extracted molecule total RNA
Extraction protocol RNA was extracted with Rneasy mini kit (Qiagen)
Label Biotin
Label protocol Biotinylated complementary RNAs (cRNAs) were synthesized in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction.
 
Hybridization protocol The biotinylated cRNAs were cleaned up, fragmented, and hybridized to the rhesus macaque expression arrays at 45°C for 16 h with constant rotation at 60 rpm. The gene chips were then washed and stained with Affymetrix fluidics stations 450.
Scan protocol The gene chips were scanned on Affymetrix scanner 3000
Data processing The images are processed to collect raw data with GeneChip Operating Software (GCOS) 1.4.
.CEL files were loaded in to Genespring GX10 software, data was preprocessed with RMA (Robost Multichip Analaysis) and per gene normaization was performed by setting measurements to median.Only those transcripts that were called present or marginal in at least one of the same condition were taken into account. Genes with statistically significant differences between the SIV infected, PD-1 antibody treated versus SIV infected, Control antibody treated group of Rhesus macaques were classified(One way ANOVA, p-value cutoff 0.05) with minimum of 1.5 fold change difference.
 
Submission date Nov 23, 2011
Last update date Apr 27, 2012
Contact name RAVI DYAVAR SHETTY
E-mail(s) rdyavar@emory.edu
Phone 404-727-9233
Organization name emory university
Department Microbiology and Immunology
Lab Rama Amara
Street address 954 Gatewood RD NE
City Atlanta
State/province Georgia
ZIP/Postal code 30329
Country USA
 
Platform ID GPL3535
Series (1)
GSE33933 Gene expression in the blood of SIV infected Rhesus macaques following in vivo PD-1 blockade

Data table header descriptions
ID_REF
VALUE rma normalized

Data table
ID_REF VALUE
AFFX-BioB-5_at 0.24956131
AFFX-BioB-M_at 0.11750507
AFFX-BioB-3_at 0.10992718
AFFX-BioC-5_at 0.12019253
AFFX-BioC-3_at 0.073293686
AFFX-BioDn-5_at 0.08351898
AFFX-BioDn-3_at -0.00685215
AFFX-CreX-5_at -0.02882576
AFFX-CreX-3_at -0.07928753
AFFX-DapX-5_at 0.27169943
AFFX-DapX-M_at 0.29441547
AFFX-DapX-3_at 0.5691309
AFFX-LysX-5_at 0.50588465
AFFX-LysX-M_at 0.48785067
AFFX-LysX-3_at 0.73748875
AFFX-PheX-5_at 0.5949745
AFFX-PheX-M_at 0.5409894
AFFX-PheX-3_at 0.4834876
AFFX-ThrX-5_at 0.10567093
AFFX-ThrX-M_at 0.55203676

Total number of rows: 52865

Table truncated, full table size 1708 Kbytes.




Supplementary file Size Download File type/resource
GSM838989.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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