|
| Status |
Public on Aug 09, 2012 |
| Title |
CD4mem_CP_minus7PCD_Rh23166 |
| Sample type |
RNA |
| |
|
| Source name |
Sorted CD8+ and CD4+ memory T cells of mononuclear cell preparation from lymph nodes
|
| Organism |
Macaca mulatta |
| Characteristics |
subject: Rh23166
cohort: PC125B
lav: SIV_239_dNef
protection: CP
group: B
tissue: lymph node
sort: CD4mem
time: minus7PCD
barcode: 6247258071_B
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy Micro Kits (Qiagen) according to the manufacturer’s protocol. The isolated total RNA was checked for quantity and quality using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.
|
| 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 to Human HT12 V4 BeadChips (Illumina) at 58°C for 20 hours.
|
| Scan protocol |
The arrays were scanned using Illumina’s iSCAN and quantified using Genome Studio (Illumina).
|
| Description |
CD4mem T cells sort from CP animal at minus7PCD
|
| Data processing |
Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation. Technical replicates were PC225)
software packages and versions: R 2.14.12; Biobase 2.14.0; Limma 3.10.3; impute 1.28.0; bioDist 1.26.0; ComBat (unversioned, downloaded March 2010 from http://www.bu.edu/jlab/wp-assets/ComBat/Download.html)
|
| |
|
| Submission date |
Aug 08, 2012 |
| Last update date |
Mar 25, 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 (2) |
| GSE39968 |
Transcriptional profiles of sorted CD8+ and CD4+ memory T cells from CP and NP and unvaccinated control RM 7 days prior to, and 4 and 14 days after wt SIVmac239 challenge by microarray analysis. |
| GSE40006 |
Lymph node T cell responses predict the efficacy of live attenuated SIV vaccines |
|
