|
| Status |
Public on May 14, 2024 |
| Title |
WT 1 600ug/mL s1 calprotectin |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: Newman
cell type: Bacteria
genotype: WT
treatment: 600ug/mL s1 calprotectin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN RNeasy
NEBNext Ultra II RNA Library Prep kit for Illumina and NEBNext Multiplex Oligos for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Bioinformatic analysis was performed using CLC Genomics Workbench Software. Paired-end sequencing data in fastq.gz format were imported into CLC Genomics Workbench and trimmed to remove barcodes and adapter sequences. The remaining ribosomal RNA reads were depleted computationally by aligning all reads to a sequence list containing all rRNA sequences for the Staphylococcus aureus genome (NC_009641). Unmapped (non-rRNA) reads were collected and utilized for “RNA-seq analysis” function (standard settings, similarity fraction of 0.8) to generate expression values for each gene.
Assembly: Staphylococcus aureus genome (NC_009641)
Supplementary files format and content: Excel file with differential expression against vehicle for all the strains. Included Log2 fold change and P-value
|
| |
|
| Submission date |
Apr 26, 2024 |
| Last update date |
May 14, 2024 |
| Contact name |
Eric P Skaar |
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Pathology, Microbiology, and Immunology
|
| Lab |
Eric Skaar
|
| Street address |
1161 21st Avenue South
|
| City |
Nashville |
| State/province |
Tennessee |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL27158 |
| Series (1) |
| GSE265954 |
The coordinated adaptation of Staphylococcus aureus to calprotectin dependent metal sequestration [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN41096181 |
| SRA |
SRX24380067 |
