|
| Status |
Public on Jul 29, 2022 |
| Title |
NO3_WT rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Actinobacillus pleuropneumoniae serovar 1 str. 4074 |
| Characteristics |
tissue: Bacteria
strain: str. 4074
genotype: wild type
treatment: anaerobic culture, supplemented with 5mM nitrate
|
| Treatment protocol |
Supplemented with or without NaNO3 (5 mM)
|
| Growth protocol |
Strains WT, ΔnarQ, and ΔnarP were cultured to mid-log phase (4 h) at 37°C in TSB-NAD (10 μg/mL) medium in an anaerobic condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from strains WT, ΔnarQ, and ΔnarP cultured to mid-log phase supplemented with or without NaNO3 (5 mM) in anaerobic conditions. 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.
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 NextSeq 500 |
| |
|
| Data processing |
Data filtering and quality control were performed by Cutadapt and FastQC to remove reads with an average quality score below Q20.
High-quality clean reads were aligned to the A. pleuropneumoniae 4074 genome (NZ_CP029003.1) by Bowtie2.
The raw expression levels of the genes were counted using HTSeq 0.6.1p2 (union protocol), and the expression levels were normalized using FPKM. Analysis of sequencing RPKM saturation using RSeQC.
Assembly: Actinobacillus pleuropneumoniae serovar 1 str. 4074 (NZ_CP029003.1)/ASM17849v2
Supplementary files format and content: Bam files contain the sequence alignment information of the filtered reads and the reference genome
Supplementary files format and content: Microsoft Excel file contains reads count and FPKM for all samples
|
| |
|
| Submission date |
Jul 05, 2022 |
| Last update date |
Jul 29, 2022 |
| 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 |
GPL32420 |
| Series (1) |
| GSE207497 |
Effects of two-component system NarQ/P deletion on gene expression of Actinobacillus pleuropneumoniae in nitrate-rich anaerobic growth |
|
| Relations |
| BioSample |
SAMN29504636 |
| SRA |
SRX16027093 |
