|
| Status |
Public on Dec 17, 2022 |
| Title |
KO_1 |
| Sample type |
SRA |
| |
|
| Source name |
USA300 LAC
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA300 LAC
genotype: narG knockout
treatment: growth phase
|
| Treatment protocol |
All the strains were grown to the stationary-phase (OD600 = 0.5).
|
| Growth protocol |
Overnight cultures of narG knockout mutant and S. aureus wild-type strains were diluted in TSB medium (OD600 = 0.05)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TTotal RNA was extracted from S. aureus strains by CTAB method and the RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 2μg of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
All of the analyses were performed using the free online platform of Majorbio Cloud Platform
High-quality reads in each sample were mapped to the reference genome using Bowtie2.
In this step, randomly selected 10000 raw reads in each sample are aligned to Rfam database. Based on the annotation results, percentage of rRNA in each sample is calculated, which is estimated as rRNA contamination.
Quantify gene and isoform abundances from single-end or paired-end RNA-Seq data using RSEM, Kallisto, and Salmon.
Goatools is used to identify statistically significantly enriched GO term using Fisher’s exact test.
KOBAS 2.0 is used to identify statistically significantly enriched pathway using Fisher’s exact test.
Assembly: Staphylococcus aureus NCBI genome JAFFHX000000000.1
Supplementary files format and content: DEG-WT_vs_KO_20221213.txt
|
| |
|
| Submission date |
Dec 13, 2022 |
| Last update date |
Dec 17, 2022 |
| Contact name |
Yujie Li |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Science and Technology of China
|
| Street address |
1129 Huizhou Ave
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
23005 |
| Country |
China |
| |
|
| Platform ID |
GPL27158 |
| Series (1) |
| GSE220798 |
NarGHJI mediated virulence in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN32187100 |
| SRA |
SRX18665897 |
