|
| Status |
Public on Apr 25, 2023 |
| Title |
emm87 - 1057-2 - biol rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Streptococcus pyogenes |
| Characteristics |
cell type: bacteria
strain: TSPY1057
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extract with QIAGEN Rneasy mini kit. 500 ng of total RNA was used as input for downstream libraries
RNA-Seq libraries were completed by the University of Texas MD Anderson Cancer Center Core Genomic Center (ATGC)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Untrimmed, paired-end 75-bp reads were QC'd with fastqc-v0.11.8
Untrimmed reads were aligned using STAR-v2.7.9a with default parameters to each respective emm-type reference
HTSeq-v0.11.0 was used to enumerate read counts
DESeq2 package-v1.30.1was used to perform differential gene expression analysis on normalized read counts using the DESeq2 median of ratios read normalization method
Supplementary files format and content: comma separated value files with normalized read counts and fold change results
|
| |
|
| Submission date |
Apr 20, 2023 |
| Last update date |
Apr 25, 2023 |
| Contact name |
William Charles Shropshire |
| E-mail(s) |
wcshropshire@mdanderson.org
|
| Phone |
8307082542
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Street address |
1901 East Road
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL28678 |
| Series (1) |
| GSE230158 |
Identification of Distinct Impacts of CovS Inactivation on the Transcriptome of Acapsular Group A Streptococci |
|
| Relations |
| BioSample |
SAMN34266003 |
| SRA |
SRX20026144 |
