NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1039745 Query DataSets for GSM1039745
Status Public on Dec 07, 2012
Title HIV-1 Vpr (1) [mRNA]
Sample type RNA
 
Source name Primary human Neurons
Organism Homo sapiens
Characteristics treatment: Vpr
Treatment protocol Cells were treated with Vpr (10 pg/ml) 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 Gene expression profiling that was performed using the Affymetrix GeneChip® [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Label biotin
Label protocol Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.
 
Hybridization protocol Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.
Scan protocol Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.
Description SAMPLE 3
Data processing RMA normalization using GeneSpring software.
Quality control measures were carried out to ensure that RNA isolated was not degraded or lost. Housekeeping control genes and spike controls were routinely analyzed on the GeneChip® microarrays to confirm the successful labeling of target RNAs. Preliminary data analysis was performed in conjunction with the Thomas Jefferson University Bioinformatics Program.
GeneChip® array results were also correlated with the array design and annotation information using the NetAffxTM Analysis Center. Hierarchical cluster analysis and heat maps were generated using Spotfire DecisionSite 7.2.
 
Submission date Nov 20, 2012
Last update date Sep 01, 2016
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 GPL6244
Series (1)
GSE44266 Deregulation of microRNAs by HIV-1 Vpr protein leads to the development of neurocognitive disorders.
Relations
Reanalyzed by GSE86357

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
7896738 4.234806
7896740 21.43025
7896742 45.0756
7896744 15.34898
7896746 264.4223
7896748 111.7506
7896750 51.00497
7896752 360.1063
7896754 35.05691
7896756 23.5609
7896759 20.00381
7896761 62.93555
7896779 58.13307
7896798 45.0909
7896817 52.56153
7896822 59.12342
7896859 27.59149
7896861 0.3608337
7896863 70.97932
7896865 52.01233

Total number of rows: 33297

Table truncated, full table size 550 Kbytes.




Supplementary file Size Download File type/resource
GSM1039745_S3_9_25_09.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap