|
| Status |
Public on Sep 17, 2020 |
| Title |
UA159 Control 2 |
| Sample type |
SRA |
| |
|
| Source name |
Streptococcus mutans UA159 wild type
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
genotype/variation: wild type
culture: Cells were grown to OD600 of 0.4, then harvested by centrifugation. Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use
|
| Treatment protocol |
At the desired OD600, samples were split in two. Control samples were incubated an additional 5 minutes. H2O2 samples were exposed to 0.5mM H2O2 for 5 mintues.
|
| 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 barcoes 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 |
S. mutans UA159 grown to OD600 = 0.4 in BHI medium Replicate 2
|
| 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 list the numbers of reads for each gene of the S. mutans genome (SMU).
|
| |
|
| Submission date |
Sep 16, 2020 |
| Last update date |
Sep 20, 2020 |
| 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) |
| GSE158080 |
The impact of H2O2 exposure on the transcriptome of Streptococcus mutans wild type and perR mutant strains |
|
| Relations |
| BioSample |
SAMN16183394 |
| SRA |
SRX9135245 |
