|
| Status |
Public on Dec 15, 2020 |
| Title |
6303299045_E: Immune non-Responder (INR) |
| Sample type |
RNA |
| |
|
| Source name |
Immune non-Responder (INR)
|
| Organism |
Homo sapiens |
| Characteristics |
subject: T049V09002318
group: INR
tissue: Whole Blood
cell type: CD4 T cells
|
| Treatment protocol |
Individuals were treated for at least 2-3 years with plasma HIV RNA levels below detectable levels using routine clinical assays; typically, less than 50 copies per milliliter. Transient blips in HIV RNA levels did not exclude participation if flanked by levels below limits of detection.
|
| Growth protocol |
Whole blood was collected from Immune Responder and Non-Responder HIV-infected ART-treated individuals and gene array analysis was performed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood was collected from Immune Responder and Non-Responder HIV-infected ART-treated individuals. Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software. Analysis of the genome array output data was conducted using the R statistical language and the Limma statistical package from Bioconductor.
|
| Label |
Biotin
|
| Label protocol |
The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.
|
| |
|
| Hybridization protocol |
Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).
|
| Scan protocol |
The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).
|
| Description |
CD4 T cells <350/µL
|
| Data processing |
Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.
|
| |
|
| Submission date |
Jan 15, 2020 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Rafick Pierre-Sekaly |
| E-mail(s) |
rafick.sekaly@case.edu, rafick.sekaly@emory.edu
|
| Organization name |
Case Western Reserve University
|
| Department |
Pathology
|
| Street address |
2103 Cornell Avenue
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE143742 |
Senescence and TGF-β producing Tregs drive HIV persistence and impaired immune homeostasis |
|
