|
| Status |
Public on Sep 19, 2022 |
| Title |
3 WT biofilm + macrophages |
| Sample type |
SRA |
| |
|
| Source name |
USA 300 LAC
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA 300 LAC
treatment: murine in vitro bone marrow-derived macrophages
|
| Treatment protocol |
4-day-old biofilm was co-cultured with medium alone, mouse in vitro-derived G-MDSCs, and/or mouse in vitro-derived macrophages for 2 hours.
|
| Growth protocol |
S. aureus biofilms were grown in static conditions at 37 degrees Celsius on human plasma-coated 12-well plated in biofilm medium (RPMI + 10%FBS + 1% L-glutamine + 1% HEPES) with daily medium replinishment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using beat-beating and TRIzol Reagent (Invitrogen) according to manufacturer's instructions.
RNA sequencing libraries were prepared beginning with 250 ng of total RNA using a ScriptSeq Complete Kit (Bacterial) – Low Input protocol (Cat. No. SCL6B, Epicentre Technologies, Madison, WI). The protocol was performed as recommended by the manufacturer with the following modification at step 3.B.1. In order to remove both eukaryotic and prokaryotic ribosomal RNA from the total preparation, instead of using 2 ul of kit provided bacterial rRNA removal solution, 1 ul of RiboZero human / mouse / rat removal solution was mixed with 1 ul of the bacterial rRNA removal solution. In addition to the above, AMPure bead purification of rRNA-depleted sample was used in step 3.D.2 of the protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Data were processed utilizing STAR as the aligner and RSEM as the tool for annotation and quantification of gene levels.
Assembly: Staphylococcus aureus subsp. aureus USA300 FPR3757
Supplementary files format and content: Excel files give normalized expression abundance in TPM and FPKM values for all the available genes.
|
| |
|
| Submission date |
Sep 14, 2022 |
| Last update date |
Sep 20, 2022 |
| Contact name |
Tammy Kielian |
| E-mail(s) |
tkielian@unmc.edu
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Pathology & Microbiology
|
| Street address |
985900 Nebraska Medical Center
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68198 |
| Country |
USA |
| |
|
| Platform ID |
GPL24034 |
| Series (1) |
| GSE213381 |
S. aureus biofilm transcriptome following G-MDSC or Macrophage co-culture |
|
| Relations |
| BioSample |
SAMN30859872 |
| SRA |
SRX17583261 |
