NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5226288 Query DataSets for GSM5226288
Status Public on Sep 17, 2021
Title EV_37_C
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: 37˚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
24_S24
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 SAMN18618694
SRA SRX10513408

Supplementary file Size Download File type/resource
GSM5226288_37_C.xlsx 63.6 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap