|
| Status |
Public on Jul 31, 2021 |
| Title |
10M3 |
| Sample type |
RNA |
| |
|
| Source name |
PAM collected from the piglets with Mhp infection
|
| Organism |
Sus scrofa |
| Characteristics |
agent: Mhp
|
| Treatment protocol |
Briefly, piglets were sedated using a Ketamine/Azaperone pre-medication mix and anaesthetized with Ketamine/Midazolam. Anesthesia throughout the procedure was maintained using Sevoflurane. PAMs were collected by broncho alveolar lavage (BAL) through an intubation with an air flow access. The lung segments were flushed in each animal using 2× 20 ml PBS. Fluid recovery was between 60–80%. Cells were collected by centrifugation for 10min at 800g from the BAL fluid and frozen at -80℃。 T
|
| Growth protocol |
All animal experiments were approved by the Science and Technology Agency of Jiangsu Province. Approval was also granted by the Jiangsu Academy of Agricultural Sciences Experimental Animal ethics committee. All efforts were made to minimize the suffering of the animals. Five-week-old piglets were purchased from a healthy herd and were identified as negative for PCV, PRRSV and Mph. All piglets were randomly divided into four groups (six piglets for each group), which included the control group, PRRSV-infected group, Mph-infected group and the Mph-PRRSV coinfected group. Animals were given commercial feed and water at libitum throughout the experiment. The piglets in the PRRSV-infected group and coinfected group were infected with the HP-PRRSV NJGC strain (106.0TCID50/mL) through intranasal (2 mL) inoculation. Mph challenge, piglets in the Mph-infected group and the coinfected group were inoculated intranasally (5 mL) with Mph XLW-1 at a concentration of 1 ×105 CCU (color change unit)/mL.The piglets in the control group received PBS (2 ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
5 mg cRNA was reverse transcribed to cDNA, fragmented, and then labeled with Cy3-dCTP (GE Healthcare) using Klenow.
|
| |
|
| Hybridization protocol |
Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit
|
| Scan protocol |
Array scanning using the Agilent Scanner G2505C.Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.
|
| Description |
GEO_10M3
|
| Data processing |
Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 24 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Genes that have values greater than or equal to lower cut-off: 50.0 in 1 out of 24 samples (“All Targets Value”) were chosen for data analysis. Significant differentially expressed genes were identified through Volcano Plot filtering. Pathway Analysis and GO analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show distinguishable gene expression profiling among samples.
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| |
|
| Submission date |
Jul 29, 2021 |
| Last update date |
Jul 31, 2021 |
| Contact name |
Bin Li |
| E-mail(s) |
libinana@126.com
|
| Phone |
86-025-84390748
|
| Organization name |
Jiangsu Academy of Agricultural Sciences
|
| Department |
Institute of Veterinary Medicine
|
| Street address |
50# Zhongling Street
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210014 |
| Country |
China |
| |
|
| Platform ID |
GPL30453 |
| Series (1) |
| GSE181105 |
Co-infection wtih porcine reproductive and respiratory syndrome virus (PRRSV) and M. hyopneumoniae (Mhp) enhances pathogenicity by upregulation of inflammatory response in piglets |
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