|
| Status |
Public on May 14, 2021 |
| Title |
E. faecalis ∆dhhP grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35. Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
∆dhhP (∆OG1RF_10010; RS0060)
|
| Organism |
Enterococcus faecalis |
| Characteristics |
genotype/variation: {delta}dhhP ({delta}OG1RF_10010; RS0060)
|
| Growth protocol |
Cells were grown to OD600 of 0.35, then harvested by centrifugation. Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Harvested cells were resuspended in 1mL of RNA Protect Bacteria Reagent (Qiagen). 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 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 |
| |
|
| Description |
∆dhhP 2
|
| 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.
Genome_build: 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 |
May 13, 2021 |
| Last update date |
May 14, 2021 |
| 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 |
GPL29473 |
| Series (1) |
| GSE174381 |
The impact of c-di-AMP levels on gene expression in Enterococcus faecalis |
|
| Relations |
| BioSample |
SAMN19159403 |
| SRA |
SRX10866720 |
