|
| Status |
Public on May 31, 2023 |
| Title |
WT_PK rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Actinobacillus pleuropneumoniae serovar 1 str. 4074 |
| Characteristics |
tissue: Bacterial culture
strain: serovar 1 str. 4074
genotype: wild type
treatment: cultured in bottles with shaking
|
| Treatment protocol |
Cultured with shaking or in static status
|
| Growth protocol |
Strains WT and Δpga were cultured to mid-log phase at 37°C with shaking (WT_PK) or in static status (WT_BF, Δpga).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from strains WT and Δpga cultured to mid-log phase supplemented with shaking or in static status. Total RNA was extracted using Trizol lysis according to the protocol recommended by the manufacturer (Total RNA Extraction Kit, Tianmo Biotech, Beijing, China), with three replicates per condition group.
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 |
| |
|
| Data processing |
Data filtering and quality control were performed by Trimmomatic and FastQC to remove reads with an average quality score below Q20.
Mapping of high-quality sequences based on the Burrows-Wheeler method to the A. pleuropneumoniae 4074 genome (NZ_CP029003.1).
The RPKM (Reads per Kilobase per Million Reads) value was used as the index of gene expression.
Assembly: Actinobacillus pleuropneumoniae serovar 1 str. 4074 (NZ_CP029003.1)/ASM17849v2
Supplementary files format and content: reads counts and RPKM values for each sample
|
| |
|
| Submission date |
Dec 30, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
Qiuhong Zhang |
| E-mail(s) |
zhangqiuhong@webmail.hzau.edu.cn
|
| Phone |
13297978781
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
No. 1, Shizishan Street
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL32988 |
| Series (1) |
| GSE221940 |
Comparative transcriptome analysis reveals metabolic differences between planktonic and biofilm of Actinobacillus pleuropneumoniae. |
|
| Relations |
| BioSample |
SAMN32512762 |
| SRA |
SRX18895375 |
