|
| Status |
Public on Aug 09, 2012 |
| Title |
CP_14PCD_Rh22741 |
| Sample type |
RNA |
| |
|
| Source name |
Mononuclear cell preparation from lymph nodes
|
| Organism |
Macaca mulatta |
| Characteristics |
subject: Rh22741
cohort: PC125
lav: SHIV_89.6
protection: CP
group: A
tissue: lymph node
cell type: Mononuclear cell preparation
time: 14PCD
barcode: 5038737001_A
|
| 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 RefSeq-8 V3 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 |
LN from CP animal at 14PCD
|
| 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 averaged. Batch correction (ComBat) was applied to correct for the cohort effect (PC125 vs. 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 |
GPL6883 |
| Series (2) |
| GSE39967 |
Transcriptional profiles of unfractionated lymph nodes cells obtained from completely protected, non protected and unvaccinated control rhesus macaques seven days prior to, and four and fourteen days after wt SIVmac239 challenge by microarray analysis. |
| GSE40006 |
Lymph node T cell responses predict the efficacy of live attenuated SIV vaccines |
|
