|
| Status |
Public on Nov 30, 2021 |
| Title |
WT_SP1 |
| Sample type |
SRA |
| |
|
| Source name |
S. aureus USA300_FPR3757 wild-type in stationary phase 1
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA300_FPR3757
phase: stationary
|
| Treatment protocol |
Bacterial cells were collected in dfferent growth phases
|
| Growth protocol |
S. aureus USA300_FPR3757 grow in TSB medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using an RNApure Bacteria Kit (CwBIO, Jiangsu, China)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S. aureus USA300_FPR3757 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: S. aureus USA300_FPR3757
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM value for every gene and every sample
|
| |
|
| Submission date |
Nov 26, 2021 |
| Last update date |
Nov 30, 2021 |
| Contact name |
Qiang Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
West China Hospital, Sichuan University
|
| Street address |
Guoxue street 37
|
| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL25144 |
| Series (1) |
| GSE189644 |
Identification and application of a panel of constitutive promoters for gene overexpression in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN23458236 |
| SRA |
SRX13238536 |
