|
| Status |
Public on Feb 14, 2017 |
| Title |
PBMCs_vacci_24h_biological rep2 [exon-level] |
| Sample type |
RNA |
| |
|
| Source name |
PBMCs at 24 h post PRRSV vaccination
|
| Organism |
Sus scrofa |
| Characteristics |
immunization status: Vaccinated
breed: German Landrace
gender: Female
|
| Treatment protocol |
PBMCs were isolated from anticoagulated blood samples collected within three days following PRRSV vaccination in 28 days old German Landrace pigs and age-matched unvaccinated pigs
|
| Growth protocol |
Piglets were housed at research station at Frankenforst, University of Bonn, Germany and maintained with standard feeding and husbandry protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted from PBMCs using the miRNeasy mini kit (P/N 217004, Qiagen, Hilden, Germany) along with on column Dnase treatment (P/N 79254, Qiagen, Hilden, Germany)
|
| Label |
biotin
|
| Label protocol |
The biotin-labeled probes (sense-strand cDNA) were prepared for microarray hybridization using the GeneChip® WT PLUS Reagent kit (P/N 902281; Affymetrix Inc., Santa Clara, CA, USA)
|
| |
|
| Hybridization protocol |
The hybridization of microarray probes followed by washing and staining was performed with the GeneChip® Hybridization, Wash and Stain kit (P/N 900720, Affymetrix Inc., Santa Clara, CA).
|
| Scan protocol |
Arrays were scanned by the Affymetrix GeneChip® scanner 3000 7G. The Affymetrix GeneChip® Command Console™ (AGCC) software was used to evaluate the array images and to export the reports of spot intensity data in .CEL file format.
|
| Description |
prrsv_24h_vac2.CEL
|
| Data processing |
Normalization and statistical analyses of microarray dataset were performed using packages of Bioconductor-platform implemented in R-project software (v3.1.2). The ‘oligo’ package was implemented for the RMA (Robust Multi-array Average) based quantile normalization of microarray data. The transcript level matrix was generated using core and the exon level matrix was generated using the probeset as target option. The differential gene expression analysis was performed using the linear analysis of microarray technique from the ‘limma’ package with empirical Bayes adjustment to the variance, followed by Benjamini and Hochberg (BH) correction for multiple testing. Genes with an FDR≤5% and a fold-change ≥1.5 were selected. In addition, To characterize the differences of transcriptional responses between pigs of vaccinated and unvaccinated group, the annotated gene expression profiles of PBMCs were subjected to an exploratory functional analysis through gene set enrichment analysis (GSEA) algorithm implemented in GSEA-P tool.
PorGene-1_0-st‐v1
PorGene-1_0-st-v1.na34.sscr2.transcript.csv (for gene-level) and PorGene-1_0-st-v1.na34.sscr2.probeset.csv (for exon-level)
Each column header represents one array sample. The left mostrow of the matrix-gene represents the transcript IDs and left most row of the matrix-exon represent the exon IDs. Values in each cells of both matrices represent the log2 transformed normalized expression of gene or exon for the corresponding row.
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| |
|
| Submission date |
Feb 24, 2016 |
| Last update date |
Feb 14, 2017 |
| Contact name |
Chritiane Neuhoff |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Bonn
|
| Department |
Institute of Animal Science
|
| Lab |
Animal Breeding and Husbandry group
|
| Street address |
Endenicher Allee 15
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21514 |
| Series (1) |
| GSE78254 |
Deciphering transcriptome profiles of porcine PBMCs in response to porcine reproductive and respiratory syndrome virus vaccine |
|
| Relations |
| Alternative to |
GSM2070467 (gene-level analysis) |
