|
| Status |
Public on Aug 01, 2013 |
| Title |
CM rAd_LCMV 94 |
| Sample type |
RNA |
| |
|
| Source name |
CD8+ T cells from mouse spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: CD8+ T cells
subset: CM
vaccine: rAd_LCMV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad Laboratories). Total RNA was then amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol. This protocol involves a first cDNA synthesis step followed by in vitro transcription for cRNA synthesis.
|
| Label |
Biotin
|
| Label protocol |
The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct Hybridization protocol
|
| |
|
| Hybridization protocol |
The biotinylated cRNA was hybridized onto Illumina Mouse Chips at 58 °C for 20 h.
|
| Scan protocol |
The arrays were scanned using an Illumina BeadStation 500GX scanner and Illumina BeadStudio v3 software. Illumina probe data were exported from BeadStudio as raw data and screened for quality. Samples failing chip visual inspection and control examination were removed.
|
| Description |
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990071_F
|
| 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.
|
| |
|
| Submission date |
Nov 21, 2012 |
| Last update date |
Aug 01, 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 |
GPL8389 |
| Series (1) |
| GSE42459 |
CD8+ T-cell memory bears the transcriptional imprint of progressive differentiation |
|
