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Sample GSM1079565 Query DataSets for GSM1079565
Status Public on Feb 07, 2013
Title HIV-1 Vpr (V2) [miRNA]
Sample type RNA
Source name Primary human Neurons
Organism Homo sapiens
Characteristics cell type: Primary human Neurons
agent: 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 for 24 hours.
Growth protocol Primary human neurons (HN) (5 x 105) purchased from ScienCell Research Laboratories (Carlsbad, CA) 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 Agilent-019118 Human miRNA Microarray 2.0 G4470B (miRNA ID version)
Label Hy5
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 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 0.14519
NC1_00000197 31.4385
NC1_00000215 -2.04777
NC2_00079215 2.88755
NC2_00092197 -1.40921
NC2_00106057 -2.06793
NC2_00122731 -8.00727
NegativeControl -43.0753
SCorner3 5.38178
dmr_285 39.8363
dmr_3 22.6524
dmr_308 -4.35932
dmr_316 -2.69232
dmr_31a -4.91458
dmr_6 28.5189
ebv-miR-BART1-3p 2.76707
ebv-miR-BART1-5p 38.6213
ebv-miR-BART10 45.9734
ebv-miR-BART10* 15.0246
ebv-miR-BART11-3p 20.1674

Total number of rows: 817

Table truncated, full table size 17 Kbytes.

Supplementary file Size Download File type/resource
GSM1079565_V2_raw.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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