|
| Status |
Public on Jan 17, 2023 |
| Title |
E. faecalis OG1RF grown in FMC medium supplemented with 80uM FeSO4. Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
OG1RF
|
| Organism |
Enterococcus faecalis OG1RF |
| Characteristics |
strain: OG1RF
treatment: Complete medium
|
| Treatment protocol |
Cultures were harvested by centrifugation, washed in RNA Protect bacterial reagent (Qiagen) and subjected to another round of cenrtrifugation. The pellets were then stored at -80C until RNA extraction.
|
| Growth protocol |
E. faecalis OG1RF was grown to mid-log phase in the chemically defined FMC medium prepared with or without 80uM FeSO4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from homogenized E. faecalis cell lysates by acid-phenol:chloroform extractions. The nucleic acid was subjected to DNase I digestion (Ambion). The RNA was then purified using the Qiagen RNeasy colum purification kit, including an additional on-column DNase digest. Total RNA was subjected to two rounds of mRNA enrichment using the MICROBExpress Bacterial mRNA Purification kit (ThermoFisher).
cDNA libraries with unique barcodes were generated from 100ng enriched mRNA using the NEB Next UltraII Directional RNA Library Prep kit for Illumina (New England Biolabs).
Pooled libraries were subjected to RNA deep sequencing (RNA-seq) at the University of Florida Interdisciplinary Center for Biotechnology Research using the Illumina NextSeq500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read mapping was performed on a Galaxy server hosted by the University of Florida Research Computer
Map with Bowtie for Illumina was used to map the reads to the E. faecalis OG1RF genome (CP002621.1)
htseq-count was used to tabulate the reads per open reading frame
Degust was used to make final comparisons in counts between cells grown in the complete versus the metal-depleted media.
Assembly: CP002621.1
Supplementary files format and content: The processed .csv data files indicate the number of reads obtained for each open reading frame (OG1RF_xxxxx) for each sample after each of four original raw data files (.fastq) were compiled and mapped against the E. faecalis OG1RF genome (CP002621.1) using Galaxy as described above.
|
| |
|
| Submission date |
Dec 15, 2022 |
| Last update date |
Jan 18, 2023 |
| Contact name |
Jessica K Kajfasz |
| E-mail(s) |
jkajfasz@dental.ufl.edu
|
| Organization name |
University of Florida
|
| Department |
Oral Biology
|
| Lab |
Lemos-Abranches
|
| Street address |
1395 Center Drive
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL32954 |
| Series (1) |
| GSE221057 |
The impact of iron depletion on the transcriptome of Enterococcus faecalis |
|
| Relations |
| BioSample |
SAMN32250706 |
| SRA |
SRX18712371 |
