|
| Status |
Public on Oct 31, 2018 |
| Title |
111 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Sus scrofa |
| Characteristics |
treatment: HP-PRRSV
dpi: 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
whole blood samples (~2.5 ml/pig) collected from 9-week old anesthetized pigs by jugular venipuncture. Total RNA was extracted from 2.5 ml cryopreserved whole blood samples using the protocol from Fleming et al.,2018 [10] and a modified miRNA extraction kit protocol optimized according to Taxis et al., 2017 [11] for the PAXgene miRNA and MirVana miRNA isolation kit™ (Thermo Scientific, Wilmington, DE, USA). Optimization of these protocols was done to increase small RNA recovery for downstream library creation. All RNA was globin depleted to account for high levels of globin transcripts
Globin reduced total RNA for sncRNA and globin and ribo-depleted mRNA library prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Quality assessment and control were performed using FastQC and TrimGalore [15] to remove adaptors and barcodes from multiplexing. Reads with a quality score below 38 and length less than 18 or longer than 72 nucleotides were discarded. A total of 24 sequences were generated for downstream analysis.
The sequenced reads were mapped to the S.scrofa 10.2 reference genome using the Hisat2 [16] package with default settings. Annotation of gene counts was performed using FeatureCounts software package [17] coupled with an in-house created sncRNA GTF file. The in-house GTF file was based on annotations from release 21 of miRbase, GtRNAdb using tRNAscan-SE 2.0, Ensembl 84 ncRNA database, and the RTH S.scrofa 10.2 ncRNA database
differential gene expression was calculated using the DeSeq2 package with the dispersion model set as local with all other parameters set at their default values.
Genome_build: ssc10.2
Supplementary_files_format_and_content: excel workbook with tRNA and miRNA log2fc values by dpi
|
| |
|
| Submission date |
Oct 30, 2018 |
| Last update date |
Oct 31, 2018 |
| Contact name |
Laura Miller |
| E-mail(s) |
laura.miller@ars.usda.gov
|
| Organization name |
USDA-ARS-National Animal Disease Center
|
| Department |
Virus and Prion Research Unit
|
| Lab |
Building 20 Room 2819 Mail Stop 2S-209
|
| Street address |
1920 Dayton Ave
|
| City |
Ames |
| State/province |
Iowa |
| ZIP/Postal code |
50010 |
| Country |
USA |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE121980 |
Differentially expressed miRNAs and tRNA genes effect host homeostasis during highly pathogenic PRRSV infections in young pigs |
|
| Relations |
| BioSample |
SAMN10348566 |
| SRA |
SRX4957642 |
