|
| Status |
Public on Feb 02, 2024 |
| Title |
Spyo65 |
| Sample type |
SRA |
| |
|
| Source name |
throat
|
| Organism |
Streptococcus pyogenes |
| Characteristics |
cell type: Non-invasive ST28/EMM-1
|
| Treatment protocol |
N/A
|
| Growth protocol |
cultured in LIM broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using Trizol (Invitrogen) and DirectZol (Zymo Research) .
TruSeq Stranded mRNA kit with RiboZero bacterial rRNA depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Edge-Pro for alignment to Spyo09 genome as reference and quantification
DESeq2 for differential gene expression
Assembly: Spyo09 genome CP136951 and CP136852
Supplementary files format and content: A csv file including counts of each gene for all 12 isolates
|
| |
|
| Submission date |
Oct 26, 2023 |
| Last update date |
Feb 02, 2024 |
| Contact name |
Weihua Huang |
| E-mail(s) |
huangwe21@ecu.edu
|
| Phone |
2527443748
|
| Organization name |
East Carolina University
|
| Department |
Pathology
|
| Street address |
600 Moye Blvd, Brody 7S-24
|
| City |
Greenville |
| State/province |
North Carolina |
| ZIP/Postal code |
27834 |
| Country |
USA |
| |
|
| Platform ID |
GPL19982 |
| Series (1) |
| GSE246380 |
RNAseq of Group A Streptococcus clinical isolates |
|
| Relations |
| BioSample |
SAMN37718965 |
| SRA |
SRX22242383 |
