|
| Status |
Public on Aug 28, 2022 |
| Title |
P10 |
| Sample type |
SRA |
| |
|
| Source name |
pig alveolar macrophages
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Pietrain
age: 5 weeks
cell type: Alveolar macrophages
infection: Uninfected
infection/uninfected time point: 9h
|
| Treatment protocol |
PRRSV-infected and uninfected PAMs at 9 h (early), 36 h (middle) and 60 h (later) were chose to systematically investigate the effect of PRRSV infection on PAMs’ miRNAomes of different pig breeds.
|
| Growth protocol |
PAMs were isolated by lung lavage from 5-week-old and specific pathogen-free (SPF) Meishan, Landrace, Pietrain and Qingping pigs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.
Total RNA were prepared for small RNA Sequencing by Synthesis according to the procedure and standards of the Illumina Sample Preparation Protocol.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
PRRSV-uninfected 9h
microRNA
|
| Data processing |
The raw sequence reads were filtered for composition.
The presence of adaptor dimers, length, sequence repetition, and copy numbers using SOAP V2.0.
Determine conserved miRNAs, the filtered sequences were initially used to search the miRBase 18.0 with BLASTN.
MiRNAs were first filtered to retain only those with a mean expression value of at least 28 read counts between the two groups were compared.
A miRNA was labeled as differentially expressed by RNA-seq when fold-change = |log2Treatment/control| ≥1 and P-value ≤0.01.
Genome_build: miRBase 18.0
Supplementary_files_format_and_content: *RPKM.xlsx: Excel files include RPKM values for each Sample.
|
| |
|
| Submission date |
Jan 14, 2020 |
| Last update date |
Aug 28, 2022 |
| Contact name |
Xiangbin You |
| E-mail(s) |
yxb_zp0710@126.com
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Huazhong agricultural university, hongshan district, wuhan
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL9126 |
| Series (1) |
| GSE143660 |
miRNA-seq data of PAMs from 4 pig breeds |
|
| Relations |
| BioSample |
SAMN13860840 |
| SRA |
SRX7556653 |
