|
| Status |
Public on Dec 21, 2018 |
| Title |
J4211-LL (Set one) |
| Sample type |
SRA |
| |
|
| Source name |
WT used for comparison to SanCI-Erm-LL
|
| Organism |
Streptococcus anginosus |
| Characteristics |
genotype: WT
growth stage: Late logarithmic
temperature: 37 degrees C
growth medium: Todd Hewitt Broth
|
| Treatment protocol |
Cells stored in RNA-Later until RNA extraction
|
| Growth protocol |
Incubator with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysozyme followed by Trizol reagent (Life Technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols with TruSeq V2 chemistry and methods.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
J4211 WT samples with no chromosomal island
Whole bacterial cell
J4211-LL_S2
|
| Data processing |
Genesifter software was used for base-calling and alignment.
BWA Reseq PE (Targeted, GATKv3) pipeline was used to align with Streptococcus anginosus reference genome (NZ_CP012805). Pairwise analyses were done using Genesifter software and gene lists were exported as tab delimited files.
Pairwise settings were as follows: normalize to mapped reads, statistical analysis using t-test, differential genes originally shown if 1.5fold or more, narrowed to 3 fold min for final analysis, data correct using Benjamini Hochberg method.
Genome_build: NZ_CP012805
Supplementary_files_format_and_content: Genesifter output
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
Dec 21, 2018 |
| Contact name |
William Michael McShan |
| E-mail(s) |
william-mcshan@ouhsc.edu
|
| Phone |
405-271-6593
|
| Organization name |
University of Oklahoma Health Sciences Center
|
| Department |
Pharmaceutical Sciences
|
| Street address |
1110 N. Stonewall Ave.
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73117 |
| Country |
USA |
| |
|
| Platform ID |
GPL25970 |
| Series (1) |
| GSE124234 |
A Phage-Like Chromosomal Island Impacts Global Transcription Patterns and Virulence in Streptococcus anginosus |
|
| Relations |
| BioSample |
SAMN10622307 |
| SRA |
SRX5172091 |
