|
| Status |
Public on Feb 06, 2013 |
| Title |
ARV ALONE (5937302028_L) |
| Sample type |
RNA |
| |
|
| Source name |
CD45+ LIVE COLON
|
| Organism |
Macaca nemestrina |
| Characteristics |
treatment protocol: ARV alone
tissue: colon
cell type: CD45+ (clone MB4-6D6) leukocytes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD45+ (clone MB4-6D6) leukocytes were sorted from thawed colon samples. RNA isolated with Qiagen RNeasy Micro kit.
|
| 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 |
Pigtail macaque
Sample name: 5937302028_L
|
| 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 |
Nov 13, 2012 |
| Last update date |
Feb 06, 2013 |
| Contact name |
Peter A Wilkinson |
| Organization name |
Case Western Reserve University
|
| Department |
Pathology / Systems Biology & Bioinformatics
|
| Street address |
2103 Cornell Road
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44120 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE42232 |
Probiotic and Prebiotic Supplementation of Antiretroviral Therapy Improves Gastrointestinal Immunity in SIV-infected Macaques |
|
