|
| Status |
Public on Oct 01, 2023 |
| Title |
SC19, Aerobic, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Streptococcus suis |
| Characteristics |
tissue: Bacteria
cell line: streptococcus suis serovar 2
cell type: str. SC19
genotype: wild type
treatment: cultured in normoxia with shaking
|
| Treatment protocol |
Cultured in hypoxia or in normoxia.
|
| Growth protocol |
Strain SC19 was cultured to late-log phase at 37°C in hypoxia or in normoxia.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the samples was extracted using the RNA Isolation Kit (Tianmo Biotech, China).
Illumina PE RNA libraries for RNA-seq were prepared using IlluminaTruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
streptococcus suis serovar 2 str. SC19(firmicutes)
|
| Data processing |
Quality control of the high-quality RNA-seq data, read mapping, and gene expression quantification were performed using the "fastp," "STAR," and "RSEM" packages, respectively.
Analysis of differentially expressed genes (DEGs) was conducted using the "DESeq2" R package (), considering genes with q-value < 0.05 and |Log2FC| > 1 as significantly differentially expressed genes (SDEGs).
Assembly: Streptococcus suis SC19 (ASM211140v1)
Supplementary files format and content: The txt files include the reads counts and TPM values for each sample
|
| |
|
| Submission date |
Jun 26, 2023 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Hao Tang |
| E-mail(s) |
2021317010006@webmail.hzau.edu.cn
|
| Organization name |
Huazhong Agriculture University
|
| Street address |
Shizishan Street 1
|
| City |
Wuhan,Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL28677 |
| Series (1) |
| GSE235734 |
Metabolic Model of Streptococcus suis reveals the Indispensability of catabolic ornithine carbamoyltransferase ArcB for Adapting to Anaerobiosis |
|
| Relations |
| BioSample |
SAMN35984301 |
| SRA |
SRX20777246 |
