|
| Status |
Public on Apr 01, 2015 |
| Title |
CT29 |
| Sample type |
RNA |
| |
|
| Source name |
PBMC, Control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
hiv status: Seronegative
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from PBMCs was extracted with MirVana isolation kit (Applied Biosystems)
|
| Label |
FAM
|
| Label protocol |
Reverse transcription was performed using the Taqman MicroRNA Reverse Transcription kit (Applied Biosystems) following the manufacturer's instructions. Quantitative Real Time PCR was performed using Microfluidic Cards-Human MicroRNA card set v3.0 (Applied Biosystems) using the ViiA 7 Real Time PCR system, following the manufacturer's instructions and using the comparative CT and standard settings.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Data processing |
Each run was exported separately using an auto detection threshold. The data were then uploaded to RealTime StatMiner software (Integromics, PA) for further analysis. Detectability threshold for miRNA assays was set to Ct value less than or equal to 35 and at least 25% of all samples in each group. We used Grubbs method to eliminate outliers within technical replicates and Genorm method to select endogenous control that is U6-snRNA/mammU6 for normalization based on stability scoring across the samples in each group. Differentially expressed miRNA between different groups were identified using parametric t-test or LIMMA (one factor analysis) and were then sorted using Benjamini-Hochberg false discovery rate (FDR) method with adjusted p-value <0.05. The fold changes were obtained using linear RQ values.
The fold change worksheet reports low viral load/control, high viral/control, and high viral load/load viral load ratios.
|
| |
|
| Submission date |
Apr 12, 2013 |
| Last update date |
Apr 01, 2015 |
| Contact name |
Velpandi Ayyavoo |
| E-mail(s) |
[email protected]
|
| Fax |
4126245612
|
| Organization name |
Velpandi Ayyavoo
|
| Street address |
130 Desoto street, University
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL11316 |
| Series (1) |
| GSE46018 |
MicroRNA regulation and its effects on cellular transcriptome in Human Immnodeficiency Virus-1 (type-1) infected individuals with distinct viral load and CD4 cells |
|
