|
| Status |
Public on Feb 18, 2021 |
| Title |
S. mutans UA159 grown in FMC to OD600 = 0.4, then exposed to 4mM ZnSO4 for 90 minutes Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Laboratory stock
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
genotype/variation: wild type
treatment: ZnSO4 for 90min
|
| Treatment protocol |
Cells were grown to OD600 of 0.4, exposed to zinc for 90 minutes, then harvested by centrifugation. Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use
|
| Growth protocol |
Cells were grown to OD600 = 0.4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Harvested cells were resuspended in 1mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA was isolated from homogenized S. mutans 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 |
UA159 Zinc 90 minutes 3
|
| Data processing |
Read mapping was performed on a Galalxy server hosted by the University of Florida Research Computer
Map with Bowtie for Illumina was used to map the reads to the S. mutans UA159 genome (NC_004350.2)
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: NC_004350.2
Supplementary_files_format_and_content: The processed .csv data files contain comparisons of the pooled data (three replicates for each sample type if available) between two samples, represented as the log2 fold change of expression of each coding region (SMU).
|
| |
|
| Submission date |
Feb 17, 2021 |
| Last update date |
Feb 19, 2021 |
| Contact name |
Jessica K Kajfasz |
| E-mail(s) |
[email protected]
|
| 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 |
GPL29159 |
| Series (1) |
| GSE166993 |
The impact of exposure to excess zinc on the transcriptome of Streptococcus mutans |
|
| Relations |
| BioSample |
SAMN17974828 |
| SRA |
SRX10122054 |
