|
| Status |
Public on Oct 14, 2022 |
| Title |
inguinal lymph nodes, ASFV-infected, Day 41, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
inguinal lymph nodes
|
| Organism |
Sus scrofa domesticus |
| Characteristics |
tissue: inguinal lymph nodes
genotype: WT
treatment: ASFV-infected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent following manufacturer’s recommendations
RNA libraries for RNA-seq were prepared using VAHTS® Universal V6 RNA-seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke (parameter- lowQual=20,nRate=0.005,qualRate=0.5)
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 (parameter-x --no-unal --un-conc)
Read count extraction and normalization were performed using RSEM（V1.3.1）
Differential expression analysis was performed using DESeq2（parameter-FDR <0.05&log2FC>1 || log2FC<-1 ）
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 11, 2022 |
| Last update date |
Oct 25, 2022 |
| Contact name |
Changjie Lv |
| E-mail(s) |
lvcj@webmail.hzau.edu.cn
|
| Phone |
13667287676
|
| Organization name |
huazhong agriculture university
|
| Street address |
shizishan street
|
| City |
wuhan |
| State/province |
hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL29562 |
| Series (1) |
| GSE215197 |
Infection characteristics and transcriptomics of African swine fever virus in Bama mini-pigs |
|
| Relations |
| SRA |
SRX17639448 |
| BioSample |
SAMN30932908 |
