|
| Status |
Public on Dec 07, 2012 |
| Title |
Control (1)_HN [mRNA] |
| Sample type |
RNA |
| |
|
| Source name |
Primary human Neurons
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: control
|
| Treatment protocol |
Cells were treated with Tat (10 ng/ml) kindly received from NIH (AIDS reagnets Bank) for 24 hours.
|
| Growth protocol |
Primary human neurons (HN) (5 x 105) purchased from ScienCell Research Laboratories (Carlsbad, CA) 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 was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for Gene expression profiling that was performed using the Affymetrix GeneChip® [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
|
| Label |
biotin
|
| Label protocol |
Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.
|
| |
|
| Hybridization protocol |
Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.
|
| Scan protocol |
Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.
|
| Description |
CONTROL 1
|
| Data processing |
RMA normalization using GeneSpring software.
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 GeneChip® microarrays to confirm the successful labeling of target RNAs. Preliminary data analysis was performed in conjunction with the Thomas Jefferson University Bioinformatics Program.
GeneChip® 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 20, 2012 |
| Last update date |
Sep 01, 2016 |
| 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 |
GPL6244 |
| 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. |
|
| Relations |
| Reanalyzed by |
GSE86357 |
