|
| Status |
Public on Aug 20, 2020 |
| Title |
Mock_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
porcine alveolar macrophages
|
| Organism |
Sus scrofa |
| Characteristics |
cell-type: PAMs collected from 8-week-old pigs
infection: Non
days post infection: 21 dpi
|
| Treatment protocol |
The 4-week-old piglets were divided into seven groups, Among these seven groups, two groups received a HP-PRRSV-JXA1 or NADC30-like HNhx challenge, two groups were Mab-PN9cx3 treatment groups followed by challenging with HP-PRRSV-JXA1 or NADC30-like HNhx, two groups were treated with isotype Mab (2G8) followed by challenging with two PRRSV isolates, and the remaining group was included as negative control (MOCK). At minus 2-day (-2 day) -post inoculation (d.p.i.), an intravenous (I.V.) administration with 10mg of mAb-PN9cx3 or mAb-2G8 (2mg/mL in PBS) was conducted in the lateral auricular vein of each piglet in indicated groups. In all PRRSV challenge only groups, a same volume of PBS was administrated in the same route as well. All piglets except negative control were challenged at 0 d.p.i with 2 ml of the HP-PRRSV-JXA1 or NADC30-like HNhx virus stock. One day later (1 d.p.i), additional 10mg of mAb-PN9cx3 or mAb-2G8 was administrated via auricular vein for Mab-treated groups. All animals were euthanized and subjected to necropsy andPAMs harvesting at 21 d.p.i.
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bronchoalveolar lavage fluid (BALF) from piglets experimental infected by PRRSV with or without mAB treatment was collected by lung lavation with sterilized PBS.PAMs from BALF were harvested by centrifugation at 300 g for 10 min and viability of PAMs was evaluated by stained cells with trypan blue. Totally 1× 107 viable PAMs were harvested using 1 mL TRizol Reagent
For RNA-seq, mRNA was purified and RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit (non-strand specific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
No PRRSV infection, No Mab treatment
|
| Data processing |
Basecalls performed using CASAVA
For RNA-seq, Illumina sequencing reads were mapped to pig (Sus scrofa v11.1) by using Hisat2.1.0 with default settings for parameters. Kallisto_0.45.1 was used for quantifying abundance of each transcript. TPM values were calculated to measure the expression levels of gene’s transcripts. Differential expression analysis of genes was performed by Sleuth_0.30.0. Differentially expressed genes were filtered by the following parameters: TPM ≧ 1, fold-changed (FC) ≧ 2 and p-value < 0.05.
Genome_build: Sus_scrofa_v11.1
Supplementary_files_format_and_content: Tab-delimited text file includes TPM values for each RNA-seq samples.
|
| |
|
| Submission date |
Aug 19, 2020 |
| Last update date |
Aug 20, 2020 |
| Contact name |
Yuchen Nan |
| E-mail(s) |
nanyuchen2015@nwsuaf.edu.cn
|
| Organization name |
Northwest A&F University
|
| Street address |
No.22 XinongLu
|
| City |
Yangling |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE156504 |
Gene expression profiles for porcine alveolar macrophage isolated from piglets injected with Mab followed by challenge with two PRRSV strains: PRRSV-JXA1 and PRRSV-HNhx |
|
| Relations |
| BioSample |
SAMN15858754 |
| SRA |
SRX8972048 |
