|
| Status |
Public on Oct 03, 2010 |
| Title |
HIV-specific CD8 T cells_Controller_941849 |
| Sample type |
RNA |
| |
|
| Source name |
HIV-specific CD8 T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD8 T cells
clinical status: Controller
|
| Treatment protocol |
PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
|
| Scan protocol |
The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
|
| Description |
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Data processing |
The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
|
| |
|
| Submission date |
Sep 10, 2010 |
| Last update date |
Sep 16, 2010 |
| Contact name |
W. Nicholas Haining |
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Haining lab
|
| Street address |
44 Binney Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL3921 |
| Series (2) |
| GSE24081 |
Comparison of gene expression profiles of HIV-specific CD8 T cells from controllers and progressors |
| GSE24082 |
Comparison of gene expression profiles of HIV-specific CD8 T cells from controllers and progressors and Jurkat cells with or without PD-1 ligation |
|
