|
| Status |
Public on Sep 17, 2021 |
| Title |
EV_34_B |
| Sample type |
SRA |
| |
|
| Source name |
Extracellular vesicles, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: AH1263
genotype: wild-type
growth medium: TSB
growth time: 15h
growth temperature: 34˚C
|
| Treatment protocol |
EVs were stored at -20˚C prior to RNA extraction
|
| Growth protocol |
Strains were grown in TSB medium at 34˚C or 37˚C with shaking for 15h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
EVs were pelleted with ExoQuick-TC buffer and EV RNA was isolated utilizing the Aiagen miRNeasy kit ans contaminating DNA was removed by treatment with Ambion DNA-free
Libraries were created using the QIAseq FX Single Cell RNA Library kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
total RNA, non-rRNA-depleted
20_S20
|
| Data processing |
Raw data files (.fatsq) were imported into the CLC Genimics workbench (v11) software platform for analysis
Reads corresponding to RNA were filtered out and removed
Expression values were calculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped and noramlized using "quantile nornalization"
Normalized expression values were exported into excel files
Genome_build: The reference genome used for the analysis was based on NC_007793 and included annaotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary_files_format_and_content: Expression values for each gene were initially calculated as RPKM values. The RPKM values were then normalized and the "Normalized expression values"are presented in the excel files
|
| |
|
| Submission date |
Apr 05, 2021 |
| Last update date |
Sep 17, 2021 |
| Contact name |
Paul Briaud |
| E-mail(s) |
paul.briaud.pb@gmail.com
|
| Organization name |
Ohio University
|
| Street address |
107 Irvine Hall
|
| City |
Athens |
| State/province |
OH |
| ZIP/Postal code |
45701 |
| Country |
USA |
| |
|
| Platform ID |
GPL28116 |
| Series (1) |
| GSE171489 |
Temperature influences the composition and cytotoxicity of extracellular vesicles in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN18618698 |
| SRA |
SRX10513404 |
