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Sample GSM1079611 Query DataSets for GSM1079611
Status Public on Feb 07, 2013
Title HIV-1 Vpr (V2)_SH-SY5Y [miRNA]
Sample type RNA
Source name Human Neuronal Cell line
Organism Homo sapiens
Characteristics cell line: SH-SY5Y neuronal cell line
treatment: HIV-1 Vpr
Treatment protocol Cells were treated with 10 pg/ml of Vpr protein kindly received from Dr Eric Cohen, University of Montreal-Canada or with 10 ng/ml of Tat protein kindly received from NIH (AIDS reagnets Bank) 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
Label protocol Standard Agilent protocol.
Hybridization protocol Standard Agilent protocol.
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 Feb 07, 2013
Last update date Feb 12, 2013
Contact name Bassel E Sawaya
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 GPL8227
Series (1)
GSE44266 Deregulation of microRNAs by HIV-1 Vpr protein leads to the development of neurocognitive disorders.

Data table header descriptions
VALUE quantile normalized signal

Data table
DarkCorner 6.14348
NC1_00000197 4.11298
NC1_00000215 6.05291
NC2_00079215 -1.3799
NC2_00092197 1.67403
NC2_00106057 8.17956
NC2_00122731 1.90401
NegativeControl 11.2174
SCorner3 1.03163
dmr_285 4.35528
dmr_3 2.70261
dmr_308 -3.60374
dmr_316 -2.19733
dmr_31a -4.40279
dmr_6 3.7534
ebv-miR-BART1-3p -1.1284
ebv-miR-BART1-5p 5.0401
ebv-miR-BART10 8.13265
ebv-miR-BART10* 1.24501
ebv-miR-BART11-3p 2.52011

Total number of rows: 817

Table truncated, full table size 17 Kbytes.

Supplementary file Size Download File type/resource
GSM1079611_V2.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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