|
| Status |
Public on Dec 07, 2012 |
| Title |
Differentiated SH-5Y cells treated with supernatant from HIV-infected U-937 (1) [mRNA] |
| Sample type |
RNA |
| |
|
| Source name |
24 hour treated with supernatant isolated with HIV JR-FL
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: neuronal cell line SH-SY5Y
treatment: supernatant from HIV-infected U-937
|
| Treatment protocol |
Cells were treated for 24hrs with 0.1 pg/cell as calculated by p24 ELISA, of supernatant isolated from U-937-infected with HIV-1 JR-FL
|
| 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.
|
| 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).
|
| |
|
| 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-JR-FL (1)
|
| Data processing |
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 GeneAtlas® microarrays platform to confirm the successful labeling of target RNAs.
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 |
Nov 29, 2012 |
| 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 (2) |
| GSE44265 |
HIV-1 Tat protein promotes neuronal dysfunction through disruption of microRNAs. |
| GSE44266 |
Deregulation of microRNAs by HIV-1 Vpr protein leads to the development of neurocognitive disorders. |
|
