|
| Status |
Public on Jan 07, 2020 |
| Title |
HA MRSA (nm)_E_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Staphylococcus aureus |
| Characteristics |
clonal complex: 1
growth phase: Exponential
strain: clinical
|
| Treatment protocol |
No treatments were applied.
|
| Growth protocol |
overnight culture of S.aureus, diluted 1:10 and grown in fresh Brain Heart infusion Broth at 370C. Total RNA extracted during Stationary growth phase (OD600=1.0) and exponential growth phase (OD600=0.5)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with “RNeasy mini kit” (Qiagen) with additional “on-column DNase digestion”,mRNA enrichment/rRNA depletion was done using Ribo-Zero™ Magnetic Kit (Gram-Positive Bacteria) (epicentre, an Illumina company)
libraries constructed as per “Ion Total RNA-seq Kit V2” (Ion Torrrent, Life Technologies)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Total RNA
Processed_Data_N315AsReference_E.xlsx, Processed_Data_USA300AsReference_E.xlsx
|
| Data processing |
Adapter sequence trimmed data in FASTA format was exported to CLC Genomics Workbench Version 6.2.2 software.
Data quality was checked and trimmed using length (Maximum length: 200 bp and minimum length: 50 bp) and PHRED score (Reads with PHRED quality score less than 16 were excluded).
RNA-seq experiments were set up in CLC Genomics workbench software using the two references and the resulting data was normalized by count
Genome_build: two reference genomes used for analysis USA300_FPR3757 (NCBI RefSeq accession numbers NC_007793.1, NC_007790.1, NC_007791.1, NC_007792.1) and N315 strains (NCBI RefSeq accession numbers NC_002745.2, NC_003140.1)
Supplementary_files_format_and_content: Excel sheets with RPKM values included for each samples
|
| |
|
| Submission date |
Jul 08, 2015 |
| Last update date |
Jan 07, 2020 |
| Contact name |
Imalka U P K Tennakoon |
| E-mail(s) |
imalka123@yahoo.com
|
| Phone |
+61420298510
|
| Organization name |
Queensland University of Technology
|
| Department |
Institute of Health and Biomedical Innovation
|
| Street address |
60,Musk Avenue,Kelvingrove
|
| City |
Brisbane |
| State/province |
QLD |
| ZIP/Postal code |
4059 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20673 |
| Series (1) |
| GSE70636 |
Next generation sequencing allows identification of quantitave differential gene expression between four clinical strains of methicilin resistant Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN03850682 |
| SRA |
SRX1089002 |
