|
| Status |
Public on Aug 01, 2024 |
| Title |
Ctrl_A10 |
| Sample type |
SRA |
| |
|
| Source name |
NCTC 8325
|
| Organism |
Staphylococcus aureus subsp. aureus NCTC 8325 |
| Characteristics |
strain: NCTC 8325
time: 10hrs
treatment: Saline
|
| Treatment protocol |
USA400 was grown in the presence or absence of unfractionated heparin (2 ug/mL)
|
| Growth protocol |
USA400 was grown in TSB for 18-24 hours at 37°C with 200 rpm of shaking. Bacterial suspensions were diluted to a final dilution of 1:1000 and were cultured for 3 or 10hrs at 37°C with 1000 rpm of shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolated using RNeasy Mini Kit (Qiagen) following manufacturer’s recommendations followed by DNase treatment using the TURBO DNA-free Kit (Invitrogen)
RNA samples were rRNA depleted using the Ribo-Zero Plus rRNA Removal kit (Illumina) and libraries were prepared using the Illumina Stranded Total RNA Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
CLC Genomics Workbench (v.21.0.5)
Illumina reads were trimmed for adaptor sequence and for quality
Trimmed sequences were mapped to to the reference genome sequence of USA400 assembly NC_007795.1, with the parameters: mismatch cost, 2; insertion and deletion cost, 3; length and similarity fraction, 0.8.
Uniquely mapped transcripts from each sample were exported from CLC Genomics Workbench and used for normalization and differential gene expression analysis with an R package, DESeq2 version 1.34.0
Assembly: NC_007795.1
Supplementary files format and content: tab-delimited text files include uniquely mapped transcript values for each sample and time point
|
| |
|
| Submission date |
May 01, 2023 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Christophe Langouët-Astrié |
| E-mail(s) |
christophe.langouetastrie@cuanschutz.edu
|
| Organization name |
University of Colorado Denver, Anschutz
|
| Department |
Pulmonary Sciences and Critical Care
|
| Lab |
Eric Schmidt
|
| Street address |
12700 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL33368 |
| Series (1) |
| GSE231407 |
Pneumonia-induced shedding of epithelial heparan sulfate inhibits the bactericidal activity of cathelicidin |
|
| Relations |
| BioSample |
SAMN34504345 |
| SRA |
SRX20177035 |
