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Sample GSM1079564 Query DataSets for GSM1079564
Status Public on Feb 07, 2013
Title HIV-1 Vpr (V1) [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 5.24259
NC1_00000197 3.82863
NC1_00000215 3.3381
NC2_00079215 -4.4459
NC2_00092197 1.58423
NC2_00106057 9.17907
NC2_00122731 -2.31585
NegativeControl 5.39423
SCorner3 1.34007
dmr_285 0.532273
dmr_3 0.751957
dmr_308 -3.09661
dmr_316 -1.63856
dmr_31a -2.40555
dmr_6 3.19498
ebv-miR-BART1-3p -1.45159
ebv-miR-BART1-5p 3.08871
ebv-miR-BART10 9.54439
ebv-miR-BART10* 0.589831
ebv-miR-BART11-3p 0.587428

Total number of rows: 817

Table truncated, full table size 17 Kbytes.

Supplementary file Size Download File type/resource
GSM1079564_V1_raw.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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