|
| Status |
Public on Jul 01, 2012 |
| Title |
PAMs_Tongcheng_0dpi_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Pulmonary alveolar macrophages of Tongcheng at 0 dpi of HP-PRRSV infection
|
| Organism |
Sus scrofa |
| Characteristics |
gender: male
breed: Tongcheng
cell type: Pulmonary alveolar macrophage
age: 5-week-old
infection: uninfected
time: 0 dpi
|
| Treatment protocol |
The pulmonary alveolar macrophages were collected by bronchoalveolar lavage with PBS contained 5% FCS, 25% DMEM and 2 mM EDTA.
|
| Growth protocol |
Five-week-old piglets were raised in pathogen-free facilities. The infected groups were challenged with PRRSV-Wuh2 (3 ml/15 kg, 10-5 TCID50/ml) by intramuscular inoculation, with uninfected groups as control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
|
| |
|
| Hybridization protocol |
Five μg fragmented labeled cRNA was hybridized with the GeneChip Porcine Genome Array according to the standard procedures provided by the manufacturer. Chips were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix) using the standard fluidics protocol.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
|
| Description |
Tongcheng_3_0
|
| Data processing |
There are 11 paired perfect match (PM) and mismatch (MM) 25-mer probes in the Affymetrix GeneChip porcine genome array for each probeset representing a gene. The signals from these probe pairs are used to determine whether a given gene is expressed and to measure the gene expression level. The probe-pair (PM-MM) data were used to detect the expression level of genes on the array (present call, marginal call, and absent call) by MAS 5.0 (Wilcoxon signed rank test). Raw data from .CEL files were converted to gene signal files by MAS 5.0 (Ver.2.3.1).The data were normalized between slides using the quantile normalization method by R software(Ver.2.11.1.).The differentially expressed genes, classified as those with Fold changes≧2, P value≦0.05 and FDR≦0.05, were selected using the SAM software(ver.2.1).
|
| |
|
| Submission date |
Jul 07, 2010 |
| Last update date |
Jul 01, 2012 |
| Contact name |
Bang Liu |
| E-mail(s) |
liubang@mail.hzau.edu.cn
|
| Phone |
+86-027-87284140
|
| Fax |
+86-027-87280408
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL3533 |
| Series (1) |
| GSE22782 |
Pulmonary alveolar macrophages (PAMs) of Tongcheng piglets response to HP-PRRSV infection in vivo |
|
