|
| Status |
Public on May 28, 2024 |
| Title |
biofilm_arg_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
OG1RF
|
| Organism |
Enterococcus faecalis |
| Characteristics |
cell line: OG1RF
cell type: biofilm
|
| Treatment protocol |
Cells were grown with or without arginine
|
| Growth protocol |
Enterococcus faecalis OG1RF was grown in TYPS/CBM for 6 hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Planktonic and biofilm cells were collected by centrifuging and scraping cells off Aclar disks, respectively. Total RNA was harvested using a Qiagen Rneasy kit with minor modifications. Cells were resuspended in 200 μL TE buffer (10 mM Tris pH 8.0, 1 mM EDTA) supplemented with 30 mg/mL lysozyme and 500 U/mL mutanolysin and incubated at 37 oC for 10 min, after which RNA was extracted using a Qiagen RNeasy kit following manufacturer’s instructions. Lysozyme and mutanolysin were purchased from Sigma. Residual genomic DNA was removed using Turbo DNase (Ambion) following the manufacturer’s protocol for two DNase treatments (rigorous method).
TruSeq stranded libraries were constructed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
biofilm_arg_rep3_read1
|
| Data processing |
Reads were trimmed using Trimmomatic and were imported into Rockhopper for alignment and quantification of differentially expressed genes.
Assembly: NC_017316
Supplementary files format and content: tab-delimited file includes raw counts and relative abundance for each transcript in each replicate and condition
|
| |
|
| Submission date |
May 24, 2024 |
| Last update date |
May 28, 2024 |
| Contact name |
Julia Willett |
| E-mail(s) |
jwillett@umn.edu
|
| Organization name |
University of Minnesota
|
| Street address |
689 23rd Avenue SE, 4-149 Micro Research Facility
|
| City |
Minneapolis |
| State/province |
Minnesota |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL31169 |
| Series (1) |
| GSE268264 |
Arginine impacts aggregation, biofilm formation, and antibiotic susceptibility in Enterococcus faecalis |
|
| Relations |
| BioSample |
SAMN41519425 |
| SRA |
SRX24679055 |
