|
| Status |
Public on Aug 03, 2012 |
| Title |
VISA project Vancomycin intermediate sensitive clinical isolate A2 |
| Sample type |
SRA |
| |
|
| Source name |
Mid-log cells
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA300
isolate: A2
vancomycin and daptomycin susceptibility: VISA [intermediate sensitive]
|
| Growth protocol |
Cultures grown to OD600 0.7 in 20 mL of Brain Heart Infusion Broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ambion RiboPure Bacteria Kit, was used to isolate total RNA, which was enriched using the Ambion MicrobExpress kit. cDNA was made from the RNA, then paired end libraries were created using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
A2_VISA
3 biological replicates
|
| Data processing |
Data was imported into CLC Workbench 4.8
Reads under 50 nucleotides in length were discarded.
Reads were paired, using min_distance=180 and max_distance=250
Reads were trimmed, using default settings
A 'Gene Expression' experiment was conducted, using default settings and Staphylococcus aureus TCH1516 (NC_010079) as a reference.
Genome_build: NC_010079.1
Supplementary_files_format_and_content: A1_A2_stringent_USE.txt contains all mapping information. Expression values are given in RPKM. The data has been normalized using Quantile normalization, and has also been square root transformed. Statistical analyses were on Proportion, using Baggerley's test – all pairs on the normalized expression values - FDR corrected. The 'Fold Change' column is comparing fold change of A2 against A1.
|
| |
|
| Submission date |
Aug 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim Read |
| E-mail(s) |
[email protected]
|
| Organization name |
Emory University
|
| Street address |
615 Michael Street, Suite 301
|
| City |
Atlanta |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL15888 |
| Series (1) |
| GSE39868 |
A mutation in PP2C Phosphatase Gene in a Staphylococcus aureus USA300 Clinical Isolate with Reduced Susceptibility to Vancomycin and Daptomycin |
|
| Relations |
| SRA |
SRX172892 |
| BioSample |
SAMN01096599 |
