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Sample GSM1079086 Query DataSets for GSM1079086
Status Public on Feb 06, 2013
Title Primary human Neurons_Control M1 [miRNA]
Sample type RNA
 
Source name Primary human Neurons
Organism Homo sapiens
Characteristics cell type: Primary human Neurons
agent: untreated
Treatment protocol Cells were treated with Tat (10 ng/ml) kindly received from NIH (AIDS reagnets Bank) 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 06, 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)
GSE44265 HIV-1 Tat protein promotes neuronal dysfunction through disruption of microRNAs.

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
DarkCorner 12.1846
NC1_00000197 -0.748405
NC1_00000215 -0.655609
NC2_00079215 0.0788499
NC2_00092197 -2.0586
NC2_00106057 4.19342
NC2_00122731 -5.0515
NegativeControl -10.9824
SCorner3 2.53563
dmr_285 -3.92853
dmr_3 -1.9946
dmr_308 -0.250824
dmr_316 -1.78195
dmr_31a 49.0547
dmr_6 -0.384154
ebv-miR-BART1-3p -2.13036
ebv-miR-BART1-5p -1.73097
ebv-miR-BART10 2.87132
ebv-miR-BART10* 1.72098
ebv-miR-BART11-3p -1.94803

Total number of rows: 817

Table truncated, full table size 17 Kbytes.




Supplementary file Size Download File type/resource
GSM1079086_M1_raw.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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