|
| Status |
Public on Nov 23, 2021 |
| Title |
Trp-free Rif-treated wild-type, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Pure bacterial culture
|
| Organism |
Streptococcus pyogenes NZ131 |
| Characteristics |
protocol: Trp-free DMEM
genotype/variation: wild-type strain
treatment: +Rif
|
| Growth protocol |
S. pyogenes strains were cultured for 1h in the presence or absence of tryptophan in the presence or absence of rifampicin (Rif).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For S. pyogenes, total RNA was collected, DNased, and processed to remove rRNA during the RNAseq library preparation step.
NuGen Universal Prokaryotic RNA-Seq AnyDeplete kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
M_W_pos_RIF_3
|
| Data processing |
original fastq format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns), and low quality 3’ regions (Phred score < 30)
trimmed fastq files were processed by FastQC
fastq files were mapped to Streptococcus pyogenes NZ131 by CLC Genomics Workbench 12 for RNAseq analyses
read counts were modeled using Generalized Linear Model (GLM), assuming a negative binomial distribution, and reported as transcripts per million (TPM)
Wald test was used for statistical analysis of two-group comparisons
Genome_build: http://bacteria.ensembl.org/Streptococcus_pyogenes_nz131_gca_000018125/Info/Index
Supplementary_files_format_and_content: Excel file showing abundance measurements
|
| |
|
| Submission date |
Oct 26, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
Scot P Ouellette |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Pathology and Microbiology
|
| Street address |
985900 Nebraska Medical Center
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68198 |
| Country |
USA |
| |
|
| Platform ID |
GPL30892 |
| Series (1) |
| GSE174036 |
Codon-dependent transcriptional changes in response to tryptophan limitation in the tryptophan auxotrophic pathogens Chlamydia trachomatis and Streptococcus pyogenes |
|
| Relations |
| BioSample |
SAMN22567485 |
| SRA |
SRX12775900 |
