|
| 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 |
| 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. |
|
