|
| Status |
Public on Oct 10, 2014 |
| Title |
Landrace_0 dpi |
| Sample type |
SRA |
| |
|
| Source name |
lungs
|
| Organism |
Sus scrofa |
| Characteristics |
age: 35 days old
breed: Landrace
genotype: WT type
disease state: infected with HP-PRRSV
time point: 0 dpi
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pigs were dissected and the lung tissue samples were stored in liquid nitrogen. The total RNA were extracted using Trizol reagents.
Standard Illumina protocols were used to prepare the RNA libraries
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
three pigs total RNA were pooled at equal quantities
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Trim the bases with low quality (<20) from 5’end
Discard the whole reads with average quality less than 20
Clip adaptor sequence and discard reads less than 18 bp
The clean reads were mapped using BWA-0.6.2 (default set)
TMM was used to measure microRNA expression level and edgeR was used to call for differentially expressed microRNAs.
Genome_build: Ssc3
Supplementary_files_format_and_content: tab-delimited files include TMM values for each sample
|
| |
|
| Submission date |
Jun 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ning Li |
| E-mail(s) |
ninglcau@cau.edu.cn
|
| Organization name |
China Agriculture University
|
| Street address |
Yuanmingyuan West Rd. 2,Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL10945 |
| Series (1) |
| GSE58436 |
Differential microRNA expression and microRNA editing upon HP-PRRSV infection in vivo across different pig breeds |
|
| Relations |
| BioSample |
SAMN02851742 |
| SRA |
SRX592386 |
