|
| Status |
Public on Nov 20, 2020 |
| Title |
MRSA stimulated aza-derivative rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Staphylococcus aureus Methicillin-resistant
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: ATCC33592
treatment: aza-derivative 100 microM, 16 hrs
|
| Treatment protocol |
control samples were incubated for 16 hrs with DMSO 0.05%; stimulated samples were incubated with aza-derivative 100 microM for 16 hrs
|
| Growth protocol |
1x10^6 CFU/ml bacteria were grown for 16 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were collected by centrifugation (3000 rpm, 5 min) and total RNA was isolated and purified from the bacterial pellets using the GRS Total RNA Kit – Bacteria (#GK16.0100, GRISP Research Solution) following the manufacturer’s instructions. RNA-seq libraries were prepared with the TruSeq RNASample Prep kit (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
100 nucleotides of sequence was determined from both ends of each cDNA fragment using the NextSeq platform (Illumina)
Sequencing reads were annotated and aligned to the USA300 MRSA reference genome using TopHat.
results produced were checked against the Uniprot Knowledge base (https://www.uniprot.org)
Genome_build: USA300
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample, table with log2FoldChanges
|
| |
|
| Submission date |
Nov 19, 2020 |
| Last update date |
Nov 20, 2020 |
| Contact name |
PAOLA BRUN |
| Organization name |
Università di Padova
|
| Department |
Molecular Medicine
|
| Street address |
via Gabelli
|
| City |
Padova |
| State/province |
PD |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24034 |
| Series (1) |
| GSE161844 |
RNA sequencing and gene analysis of unstimulated and stimulated MRSA cultures |
|
| Relations |
| BioSample |
SAMN16842611 |
| SRA |
SRX9534696 |
