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Sample GSM404479 Query DataSets for GSM404479
Status Public on Mar 08, 2010
Title blood_SM_FUv_SIVsmm_day-5
Sample type RNA
 
Source name blood, uninfected
Organism Cercocebus atys
Characteristics gender: male
age at infection: 11.4
weight at infection (kg): 13.05
animal id: FUv
siv strain: uninfected control (SIVsm)
tissue: blood
day after infection: -5
institution: University Health Network
infection group: A
bleed date: 11-23-05
rna purification date: 10-5-07
rna purification batch: 3
hybridization batch: 2
chamber batch: 4
acquisition date: 11-6-07
Biomaterial provider Yerkes National Primate Research Center
Treatment protocol 5 sooty mangabeys and 4 rhesus macaques were inoculated intravenously with 1 ml of an uncloned strain of simian immunodeficiency virus, SIVsmm, derived from an experimentally infected SM at 11 days post-infection (1 ml of 29 plasma) as described (Gordon et al., J Immunol. 2007 Sep 1;179(5):3026-34.; Estes et al., J Immunol. 2008 May 15;180(10):6798-807.). 8 rhesus macaques were inoculated i.v. with 3000 TCID50 of SIVmac239. Blood was drawn into PaxGene RNA tubes prior to SIV infection and at post-infection times indicated.
Growth protocol All animals used in this study were housed at the Yerkes National Primate Research Center (Atlanta, GA) in accordance with the regulations of the American Association of Accreditation of Laboratory Animal Care standards. This study was approved by the Institutional Animal Care and Usage Committees (IACUC) of Emory University and the University of Pennsylvania.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the PAXgene RNA Isolation Kit according to manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNAs were prepared using a modified version of the 2-cycle Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). 5 peptide-nucleic acid (PNA) blocking oligonucleotides directed against consensus sequences in the macaque and mangabey hemoglobin I and II genes were added into the initial reverse-transcription reaction.
 
Hybridization protocol Following fragmentation, 20 micrograms of cRNA were diluted into 300 microlitres of hybridization cocktail, with 200 microlitres hybridized for 16 hr at 45 C on GeneChip Rhesus Macaque Genome Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description No additional manipulation.
GS-036 B
Data processing Data from .CEL files were analyzed using Partek Genomics Suite with RMA normalization (quantile normalization, probeset summarization, RMA background subtraction).
 
Submission date May 18, 2009
Last update date Mar 08, 2010
Contact name Steven E Bosinger
E-mail(s) bosinger@mail.med.upenn.edu
Phone 215 5735368
Fax 215 5735369
Organization name University of Pennsylvania
Department Pathology and Laboratory Medicine
Street address room 702 Stellar-Chance Laboratories, 422 Curie Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL3535
Series (1)
GSE16147 Microarray Expression Analysis of SIV infection of Sooty Mangabeys

Data table header descriptions
ID_REF
VALUE Log10 of RMA-calculated signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 2.0815
AFFX-BioB-5_at 1.81475
AFFX-BioB-M_at 2.18181
AFFX-BioC-3_at 2.12208
AFFX-BioC-5_at 1.96532
AFFX-BioDn-3_at 3.22913
AFFX-BioDn-5_at 2.85989
AFFX-CreX-3_at 3.82668
AFFX-CreX-5_at 3.57507
AFFX-DapX-3_at 3.06838
AFFX-DapX-5_at 1.5952
AFFX-DapX-M_at 2.75861
AFFX-LysX-3_at 2.63005
AFFX-LysX-5_at 1.07184
AFFX-LysX-M_at 2.00771
AFFX-Mmu-TrpnX-3_at 0.971351
AFFX-Mmu-TrpnX-5_at 1.51673
AFFX-Mmu-TrpnX-M_at 1.29704
AFFX-Mmu-actin-3_s_at 4.2008
AFFX-Mmu-actin-5_at 2.89178

Total number of rows: 52865

Table truncated, full table size 1521 Kbytes.




Supplementary file Size Download File type/resource
GSM404479.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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