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Sample GSM1064975 Query DataSets for GSM1064975
Status Public on Jan 17, 2013
Title Differentiated SH-5Y cells_Mock-(2)[mRNA]
Sample type RNA
Source name 24 hour treated with untreated
Organism Homo sapiens
Characteristics cell line: differentiated SH-SY5Y neuronal cell line
agent: untreated
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
Mock 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 4.31143
8032137 3.84808
7892906 4.22413
8005847 3.34294
7899927 4.60752
7910229 3.84239
8126952 4.32217
8148040 4.87294
8049180 4.12565
7916843 3.5804
8006573 3.39005
8095826 4.05826
8124531 4.1567
8154892 4.19517
8138045 3.37432
8061402 3.17126
7894061 3.00278
7892943 3.59887
7895548 1.21086
7895251 4.83172

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.

Supplementary file Size Download File type/resource 2.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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