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Sample GSM838271 Query DataSets for GSM838271
Status Public on Nov 23, 2011
Title HIV-1 6 [mRNA]
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics tissue: Blood
infection: HIV-1
Treatment protocol One half of the cells were subsequently infected with 0.1 MOI of virus particles using standard protocols as described and the remaining half of the culture is maintained under similar conditions and used as control. Seven days post infection (pi), cells were collected and frozen for total RNA isolation.
Growth protocol We purchased normal donor blood from the American Red Cross Blood Bank in Pittsburgh using appropriate IRB approval forms from the University of Pittsburgh. PBMCs were isolated by Ficoll-Hypaque gradient centrifugation. Freshly isolated normal donor PBMCs (5×106/mL) were stimulated with 5 µg/ml PHA-P (Sigma, St. Louis, MO) for three days. Cells were washed, divided into two parts and cultured in RPMI medium (GIBCO, CA) containing 10% FBS (Hyclone, Logan, UT), 1% L-glutamine (Cambrex, MD), 1% penicillin-streptomycin (GIBCO, CA), and IL-2 (200 U/mL, Chiron, Emoryville, CA).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the TRIzol method (InVitrogen) as suggested by the manufacturer.
Label biotin
Label protocol Total RNA samples were labeled using ‘TotalPrep RNA’ labeling kit (Ambion)
 
Hybridization protocol hybridized onto array bead chips overnight on rocker
Scan protocol scanned on ‘iScan system’ according to the manufacturer's protocols
Description Infected PBMC from donor 6
Data processing Initial raw data analysis and cubic spline normalization was done using BeadStudio Gene expression module (Illumina, Inc.).
 
Submission date Nov 22, 2011
Last update date Nov 23, 2011
Contact name Pruthvi S. R. Nagilla
E-mail(s) [email protected]
Phone 412 624-3062
URL http://www.idm.pitt.edu/directory/bios/ayyavoo.asp
Organization name University of Pittsburgh
Department Infectious Diseases and Microbiology
Street address 416 Parran Hall, 130 DeSoto Street
City Pittsburgh
State/province PA
ZIP/Postal code 15261
Country USA
 
Platform ID GPL6947
Series (2)
GSE33877 Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) [mRNA]
GSE33879 Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1)

Data table header descriptions
ID_REF
VALUE cubic spline normalization
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 60.7 0.722
ILMN_2055271 97.4 0.01186
ILMN_1736007 56.8 0.95784
ILMN_2383229 62 0.6087
ILMN_1806310 65.2 0.31357
ILMN_1779670 68.8 0.16996
ILMN_2321282 66.5 0.25165
ILMN_1671474 64.4 0.38999
ILMN_1772582 61.2 0.67852
ILMN_1735698 59.8 0.7892
ILMN_1653355 78.2 0.04216
ILMN_1717783 61.9 0.61133
ILMN_1705025 59.3 0.83004
ILMN_1814316 59.2 0.83267
ILMN_2359168 65.3 0.31094
ILMN_1731507 57 0.94862
ILMN_1787689 61.3 0.6693
ILMN_1745607 91.3 0.01449
ILMN_2136495 62.3 0.5639
ILMN_1668111 60.4 0.74045

Total number of rows: 48798

Table truncated, full table size 1178 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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