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Sample GSM1079610 Query DataSets for GSM1079610
Status Public on Feb 07, 2013
Title HIV-1 Vpr (V1)_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
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 GPL8227
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 signal

Data table
ID_REF VALUE
DarkCorner 6.22228
NC1_00000197 3.57507
NC1_00000215 12.6266
NC2_00079215 2.59259
NC2_00092197 7.4641
NC2_00106057 10.9708
NC2_00122731 5.33142
NegativeControl 26.3154
SCorner3 0.809143
dmr_285 -1.84317
dmr_3 0.561528
dmr_308 0.174289
dmr_316 -0.751688
dmr_31a -3.16198
dmr_6 0.318547
ebv-miR-BART1-3p -0.451145
ebv-miR-BART1-5p -0.935278
ebv-miR-BART10 -0.390031
ebv-miR-BART10* -0.583383
ebv-miR-BART11-3p -2.32762

Total number of rows: 817

Table truncated, full table size 17 Kbytes.




Supplementary file Size Download File type/resource
GSM1079610_V1.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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