|
| Status |
Public on Nov 20, 2023 |
| Title |
Infection, ORA_CIT, Liver4 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Liver
treatment: Infection, ORA_CIT
|
| Treatment protocol |
Preterm pigs were supplemented with intravenous/oral citrulline and inoculated with live Staphylococcus epidermidis
|
| Growth protocol |
Preterm pigs were gained by C-section and kept in NICU incubators for 14h. Pigs were nourished with standard parenteral nutrition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of homogenized liver tissues was extracted using RNeasy Mini Kit (Qiagen, Copenhagen, Denmark).
Construction of RNA-Seq libraries was done using Novogene NGS RNA Library Prep Set (PT042)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SE_ORA_CIT4
|
| Data processing |
The libraries were sequenced on the Illumina NovaSeq 6000 S4 flowcell with PE150.
Quality and adapter trimming of raw reads were performed using fastp software.
Raw data are stored in FASTQ (fq) format files which contain sequences of reads and corresponding base quality.
Alignments were performed with HISAT2 to the reference. The annotated gene information of porcine genome was obtained from Ensembl (release 109).
The featureCounts was used to generate a gene-count matrix, followed by analyses of DEGs using DESeq2 .
Assembly: Sscrofa11.1
Supplementary files format and content: xls of read counts.
Supplementary files format and content: xls of FPKM counts.
|
| |
|
| Submission date |
Nov 15, 2023 |
| Last update date |
Nov 20, 2023 |
| Contact name |
Jingren Zhong |
| E-mail(s) |
zhongjingren46@gmail.com
|
| Phone |
91819550
|
| Organization name |
University of Copenhagen
|
| Street address |
Dyrlægevej 68 DK-1870
|
| City |
Copenhagen |
| State/province |
Frederiksberg |
| ZIP/Postal code |
1870 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE247865 |
Citrulline supplementation leads to increased immune suppression and more severe outcomes in infected newborn piglets |
|
| Relations |
| BioSample |
SAMN38268838 |
| SRA |
SRX22537650 |
