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Sample GSM1195550 Query DataSets for GSM1195550
Status Public on Jul 26, 2013
Title HIV-1 Vpr SH-SY5Y (miRNA)
Sample type RNA
 
Source name SH-SY5Y neuronal cell line
Organism Homo sapiens
Characteristics cell line: SH-SY5Y
treatment: 10 pg/ml of Vpr protein
Treatment protocol Cells were treated with 10 pg/ml of Vpr protein kindly received from Dr Eric Cohen, University of Montreal-Canada for 24 hours.
Growth protocol Neuronal cell line, SH-SY5Y (5 x 105) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for miRNA array analysis using miRCURY LNATM microRNA Array, v. 11.0 (Exiqon, Woburn, MA).
Label Hy5 Power labeling
Label protocol RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).
 
Hybridization protocol RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).
Scan protocol Array chips were scanned using Axon GenePix Scanner (Molecular Devices, Downingtown, PA) and Genepix 4000 image capture software (Molecular Devices, Downingtown, PA).
Data processing Quantile normalization was used using JMP Genomics (JMP, Cary, NC) at Harvard Catalyst - Laboratory for Innovative Translational Technology (HC-LITT) and differentially regulated miRNAs were determined. Untreated cells were used as control.
 
Submission date Jul 25, 2013
Last update date Jul 28, 2013
Contact name Bassel E Sawaya
E-mail(s) sawaya@temple.edu
Phone 2157075446
Organization name Temple University
Department Neurology
Street address 3307 N. Broad Street
City Philadelphia
State/province PA
ZIP/Postal code 19140
Country USA
 
Platform ID GPL16346
Series (1)
GSE44266 Deregulation of microRNAs by HIV-1 Vpr protein leads to the development of neurocognitive disorders.

Data table header descriptions
ID_REF
VALUE quantile normalized

Data table
ID_REF VALUE
1 7.61686
2 7.294369
3 7.073135
4 6.24691
5 6.284437
6 7.202713
7 7.79845
8 6.81163
9 8.37014
10 5.943241
11 6.20146
12 7.182988
13 6.502185
14 5.794827
15 6.012065
16 7.129112
17 8.89966
18 8.803988
19 7.22867
20 7.159708

Total number of rows: 9360

Table truncated, full table size 122 Kbytes.




Supplementary file Size Download File type/resource
GSM1195550_vpr.gpr.gz 603.0 Kb (ftp)(http) GPR
Processed data provided as supplementary file

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