|
| Status |
Public on Feb 04, 2022 |
| Title |
OG1RF-M9YEM- n1 |
| Sample type |
SRA |
| |
|
| Source name |
OG1RF
|
| Organism |
Enterococcus faecalis |
| Characteristics |
growth media: M9YEM
genotype/variation: OG1RF
|
| Treatment protocol |
As indicated in the Characteristics column
|
| Growth protocol |
For growth curves and RNA preparation E. faecalis cultures were grown in M9YE base supplemented with either 20 mM glucose or mannitol. E. faecalis liquid cultures were grown at 37 °C with shaking at 25 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were resuspended in Bacteria RNA Protect (Qiagen) and incubated at room temperature for 5 min. Cells were then pelleted and stored at −80°C. Once all samples were collected, pellets were thawed, resuspended in 200 μl of Tris/EDTA-mutanolysin-lysozyme solution (10 mM Tris [pH 8.0], 1.0 mM EDTA [pH 8.0], mutanolysin [500 U ml−1], lysozyme [30 mg ml−1]), and incubated at 37°C for 10 min. To the resuspensions, 700 μl of buffer RLT (Qiagen RNeasy minikit) with 10 μl of β-mercaptoethanol (β-ME) was added, with vortexing to mix. RNA was then purified using the Qiagen RNeasy minikit according to the manufacturer's instructions. Total RNA from biological replicates was treated with TURBO DNase (Ambion/Thermo Scientific, Waltham, MA) using the rigorous protocol according to the manufacturer's instructions. DNase was removed from treated samples using the RNA Clean & Concentrator-25 (Zymo Research).
TruSeq® Stranded Total RNA Library Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq
|
| Data processing |
original fastq format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns), and low quality 3’ regions (Phred score < 30)
trimmed fastq files were processed by FastQC
fastq files were mapped to Enterococcus faecalis OG1RF by CLC Genomics Workbench 12 for RNAseq analyses
read counts were modeled using Generalized Linear Model (GLM), assuming a negative binomial distribution, and reported as transcripts per million (TPM)
Wald test was used for statistical analysis of two-group comparisons
Genome_build: Enterococcus faecalis OG1RF
Supplementary_files_format_and_content: Excel file showing fold changes and statistical significance between different growth conditions
|
| |
|
| Submission date |
Jan 28, 2022 |
| Last update date |
Feb 04, 2022 |
| Contact name |
SRIVISHNUPRIYA ANBALAGAN |
| E-mail(s) |
Srivishnupriya.Anbalagan@usd.edu
|
| Phone |
6056591482
|
| Organization name |
University of South Dakota
|
| Department |
Basic Biomedical Sciences
|
| Street address |
414 East Clark Street
|
| City |
Vermillion |
| State/province |
SD |
| ZIP/Postal code |
57069-3327 |
| Country |
USA |
| |
|
| Platform ID |
GPL29473 |
| Series (1) |
| GSE195652 |
Regulation of mannitol metabolism in Enterococcus faecalis and association with parEF0409 toxin-antitoxin locus function. |
|
| Relations |
| BioSample |
SAMN25353603 |
| SRA |
SRX13967309 |
