|
| Status |
Public on Jul 07, 2011 |
| Title |
PBMC_Pt28_HIV_Neg |
| Sample type |
RNA |
| |
|
| Source name |
HIV negative, PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood mononuclear cell (PBMC)
hiv status: negative
patient: 28
|
| Treatment protocol |
Three groups of volunteers 18 to 55 years old were enrolled in the study: HIV-infected adults receiving ART, HIV-infected adults not receiving ART, and healthy, HIV-negative adults. ART recipients were required to have received a stable regimen containing three drugs, including at least two nucleoside or nucleotide analogues, for a minimum of 12 consecutive months prior to study entry. Patients receiving protease inhibitor therapy were excluded to minimize potential confounding effects. HIV-infected participants not receiving ART could not have received any ART in the 12 months preceding study entry. Patients with a history of muscle disorder or diabetes were excluded.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were disrupted in a TissueLyser (Qiagen, Valencia, CA) prior to RNA extraction. Total RNA was isolated from PBMCs using the RNeasy Mini QIAshredder Kit, from adipose tissue using the RNeasy Lipid Tissue Mini Kit, and from muscle using the RNeasy Fibrous Tissue Mini Kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
cRNA was labelled according to the Affymetrix recommended standard protocol.
|
| |
|
| Hybridization protocol |
Labeled cRNA was hybridized to the Affymetrix FATMITO1a520158F microarray according to the manufacturer's recommended standard protocol.
|
| Scan protocol |
Hybridized huMITOchips were scanned according to the Affymetrix recommended standard protocol.
|
| Description |
GAF070515_PBMC_Pt28_HIV_Neg
|
| Data processing |
Partek Genomics Software 2.3 (Partek, St. Louis, MO) was used for statistical analysis. The raw data were normalized using the quantile normalization method. To neutralize variation by tissue, the normalized gene expression values in each tissue type were further standardized with a median-shift strategy (i.e., subtracting each gene expression value from the median expression value of the corresponding cohort). A two-way ANOVA model (i.e., tissue, disease group) was designed to identify differentially expressed genes with absolute fold change >0.5 (log2 scale) and p values <0.05. Selected genes were clustered by hierarchical clustering.
|
| |
|
| Submission date |
Jun 29, 2011 |
| Last update date |
Jul 07, 2011 |
| Contact name |
Richard A Lempicki |
| E-mail(s) |
rlempicki@mail.nih.gov
|
| Phone |
301-846-5093
|
| Organization name |
Leidos Biomedical Research, Inc.
|
| Department |
Clinical Services Program
|
| Lab |
Laboratory of Immunopathogenesis and Bioinformatics
|
| Street address |
PO Box B
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL9392 |
| Series (1) |
| GSE30310 |
HIV Infection and Antiretroviral Therapy Have Divergent Effects on Mitochondria in Adipose Tissue |
|
