NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1039746 Query DataSets for GSM1039746
Status Public on Dec 07, 2012
Title HIV-1 Vpr (2) [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 4
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 6.543192
7896740 16.95878
7896742 87.25269
7896744 28.07872
7896746 308.2609
7896748 248.2388
7896750 52.29803
7896752 365.7781
7896754 35.20349
7896756 43.38442
7896759 17.31747
7896761 73.69337
7896779 73.32912
7896798 46.94557
7896817 62.58429
7896822 77.31018
7896859 41.43974
7896861 11.08097
7896863 58.58295
7896865 55.13924

Total number of rows: 33297

Table truncated, full table size 549 Kbytes.




Supplementary file Size Download File type/resource
GSM1039746_S4_9_25_09.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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