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Sample GSM1064977 Query DataSets for GSM1064977
Status Public on Jan 17, 2013
Title Differentiated SH-5Y cells treated with HIV-1 Vpr (2)[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 (2)
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
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
VALUE RMA signal

Data table
7903292 1.22837
8032137 6.66013
7892906 9.70978
8005847 6.69452
7899927 2.42506
7910229 8.1082
8126952 9.13711
8148040 2.29722
8049180 5.9414
7916843 7.15659
8006573 6.4198
8095826 2.78896
8124531 8.12472
8154892 2.72029
8138045 8.00869
8061402 2.39549
7894061 7.30617
7892943 0.942259
7895548 9.06491
7895251 2.19532

Total number of rows: 33297

Table truncated, full table size 517 Kbytes.

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

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