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Sample GSM1064976 Query DataSets for GSM1064976
Status Public on Jan 17, 2013
Title Differentiated SH-5Y cells treated with HIV-1 Vpr (1)[mRNA]
Sample type RNA
 
Source name 24 hour treated with HIV-1 Vpr
Organism Homo sapiens
Characteristics cell line: differentiated SH-SY5Y neuronal cell line
agent: HIV-1 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 Differentiated SH-SY5Y neuronal cell line (5 x 105) 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 using Sureprep true total RNA isolation kit from Fisher scientific (#BP2800-50). RNA yield was measured on eppendorf biophotometer plus and 100 ng of total RNA was used as suggested by Affymetrix – GeneAtlas WT Expression kit manual. (Affymetrix, Santa Clara, CA), comprised of a total 33,297 probe sets. Quality control measures were carried out to ensure that RNA isolated was not degraded or lost.
Label Biotin
Label protocol Genechip WT terminal labeling kit (Affymetrix #901524) was used to label the DNA and Hybridize Affymetrix Human Gene 1.1 ST Array (#AF901626PR) using Accublock digital dry bath. Strips were washed and stained using kit (affymetrix #901667). Housekeeping control genes and spike controls were routinely analyzed on the GeneAtlas® microarrays platform to confirm the successful labeling of target RNAs.
 
Hybridization protocol Genechip hybridization control kit (Affymetrix #900454) was used as requested and described by Affymetrix.
Scan protocol The scanner is the GeneAtlas scanner and the software control is GeneAtlas Instrument Control (GAIC) v. 1.0.6.
Description Differentiated SH-5Y cells
HIV-1 Vpr
Data processing Two biological replicates were used and analysis was performed using Partek software and using RMA Statistical algorithm
GeneAtlas® 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 Jan 16, 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 GPL11532
Series (1)
GSE44266 Deregulation of microRNAs by HIV-1 Vpr protein leads to the development of neurocognitive disorders.

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
7903292 1.22697
8032137 6.66076
7892906 9.70199
8005847 6.69577
7899927 2.42902
7910229 8.09929
8126952 9.13954
8148040 2.2954
8049180 5.9468
7916843 7.15332
8006573 6.41869
8095826 2.79199
8124531 8.13521
8154892 2.7173
8138045 8.02652
8061402 2.39836
7894061 7.32234
7892943 0.938719
7895548 9.03369
7895251 2.19932

Total number of rows: 33297

Table truncated, full table size 517 Kbytes.




Supplementary file Size Download File type/resource
GSM1064976_VPRa.ga.cel.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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