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Sample GSM1079566 Query DataSets for GSM1079566
Status Public on Feb 07, 2013
Title HIV-1 Vpr_HN [miRNA]
Sample type RNA
Source name Primary human Neurons
Organism Homo sapiens
Characteristics 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 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 miRCURY LNATM microRNA Array, v. 11.0 (Exiqon, Woburn, MA).
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 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).
Description Q.NORM.1(VPR)
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 Jul 25, 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 GPL16346
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
1 1.292481
2 0
3 3.403677
6 0
7 0
8 3.821928
9 4.227664
11 1.292481
12 2.745927
13 1.292481
17 7.329329
19 0.5
20 0.5

Total number of rows: 9360

Table truncated, full table size 81 Kbytes.

Supplementary file Size Download File type/resource
GSM1079566_Vpr_raw.gpr.gz 581.5 Kb (ftp)(http) GPR
Processed data included within Sample table
Processed data are available on Series record

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