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Sample GSM1173256 Query DataSets for GSM1173256
Status Public on Jun 25, 2013
Title HIV-1 Tat (T2) [miRNA]
Sample type RNA
 
Source name SH-SY5Y_HIV-1 Tat
Organism Homo sapiens
Characteristics cell line: SH-SY5Y
cell type: human fetal neuronal cells
treated with: 10ng of HIV-1 Tat protein
Treatment protocol Cells were treated with Tat (10 ng/ml) kindly received from NIH (AIDS reagnets Bank) for 24 hours.
Growth protocol Human neuronal cell line SH-SY5Y (5 x 10^5) 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 Power labeling
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 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).
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 YL-03212013-miRNA3_0-T24b_Temple.rma-dabg-Signal
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. Sample data table includes only human miRNA (i.e. all other probes related to other species were excluded).
 
Submission date Jun 24, 2013
Last update date Jun 25, 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 GPL16384
Series (1)
GSE44265 HIV-1 Tat protein promotes neuronal dysfunction through disruption of microRNAs.

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
14q0_st 0.8274224
14qI-1_st 0.8986426
14qI-1_x_st 1.020709
14qI-2_st 0.88572
14qI-3_x_st 0.960289
14qI-4_st 0.5554811
14qI-4_x_st 0.6892848
14qI-5_st 0.9197074
14qI-6_st 0.7937266
14qI-6_x_st 0.7259426
14qI-7_st 1.023391
14qI-8_st 0.8517354
14qI-8_x_st 0.7129412
14qI-9_x_st 0.9521495
14qII-10_st 0.9841592
14qII-10_x_st 0.7758443
14qII-11_st 0.974044
14qII-11_x_st 0.7921262
14qII-12_st 0.8251257
14qII-12_x_st 1.005202

Total number of rows: 5683

Table truncated, full table size 153 Kbytes.




Supplementary file Size Download File type/resource
GSM1173256_YL_03212009_miRNA3_0_T24b_Temple.CEL.gz 757.1 Kb (ftp)(http) CEL
Processed data included within Sample table

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