|
| Status |
Public on Dec 20, 2016 |
| Title |
ABv-biological rep2 |
| Sample type |
SRA |
| |
|
| Source name |
lrgAB-ΩKm (SAB115), vancomycin, 1μg/ml (anaerobic)
|
| Organism |
Streptococcus mutans |
| Characteristics |
strain: SAB115
genotype: lrgAB mutant
culture condition: vancomycin, 1ug/ml (anaerobic)
|
| Treatment protocol |
For aerobic conditions, cultures were grown on a rotary shaker (115 rpm) without mineral oils.
For high temperature stress, cells were grown at 40°C; For vancomycin stress, cells were grown in BHI supplemeted with vancomycin at the final concentration of 1 μg/ml
|
| Growth protocol |
Cultured in BHI medium; To achieve an anaerobic condition, mineral oil was placed on top of the cultures; Cells were harvested at the mid-exponential phase of growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Collected cells were treated withRNAprotect reagent (Qiagen)
Total RNA was isolated and purified by RNeasy Mini Kits (Qiagen) with on-column digestion by RNase-free DNase I
mRNA was enriched by using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion)
cDNA libraries were constructed from the enriched mRNA samples by using NEBNext Ultra directional RNA library prep kit for Illumina and NEBNext multiplex oligonucleotides for Illumina (New England BioLabs),
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were mapped on a Galaxy server using Bowtie for Illumina (version 1.1.2)
Mapped reads per gene were counted from BAM files using htseq-count
Count-based differential expression of genes was analyzed by the R package edgeR on RStudio
Supplementary_files_format_and_content: Tab-delimited text files include DE and htseq-count values, and functional descriptions for 10 different comparisons.
|
| |
|
| Submission date |
Jul 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
SANG-JOON AHN |
| Organization name |
University of Florida
|
| Street address |
1395 Center Drive
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL21130 |
| Series (1) |
| GSE84427 |
Response of Streptococcus mutans wild type and lrgAB-deficient strains to environemntal stressors encountered in the oral cavity |
|
| Relations |
| BioSample |
SAMN05392178 |
| SRA |
SRX1949977 |
