|
| Status |
Public on Jul 20, 2024 |
| Title |
RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35873_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MGCS35873
|
| Organism |
Streptococcus dysgalactiae subsp. equisimilis |
| Characteristics |
tissue: MGCS35873
genotype: stG62647
|
| Treatment protocol |
At the desired growth stage, mid-exponential phase (OD 600nm 1.0), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation
|
| Growth protocol |
Cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using NEBNext rRNA depletion kit (NEB)
Resultant RNAs were processed using the NEBNext Ultra II directional RNA library prep kit for Illumina (NEB), reverse transcribed to cDNA, tagged with the NEBNext multiplex oligos for Illumina (NEB), pooled and sequenced
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Multiplexed libraries were sequenced on an Illumina NextSeq 500 instrument.
Reads from each pool were demultiplexed into separate fastq files corresponding to individual samples based on the inline barcodes using FASTX-toolkit.
RNA-seq reads from all strains were mapped to reference strain MGCS36044 [National Center for Biotechnology Information (NCBI) Bioproject accession number PRJNA925803], using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Differential expression (DE) analysis was performed with DESeq2 using pcaExplorer and Ideal to streamline RStudio.
DE genes were identified in each of the 38 strains compared to a common reference strain (MGCS36044).
Assembly: MGCS36044, NCBI GenBank accession GCA_029234115.1
Supplementary files format and content: EDGEpro output listing 6 space separated columns: geneID, start_coord, end_coord, average_cov, and RPKM -- determined relative to the reference MGCS36044 genome
|
| |
|
| Submission date |
Jul 11, 2024 |
| Last update date |
Jul 20, 2024 |
| Contact name |
James M. Musser |
| E-mail(s) |
[email protected]
|
| Phone |
713-441-5891
|
| Organization name |
Houston Methodist Hospital and Research Institute
|
| Department |
Pathology and Genomic Medicine
|
| Lab |
Molecular and Translational Human Infectious Disease Research
|
| Street address |
6670 Bertner Ave.
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL34696 |
| Series (1) |
| GSE272047 |
Integrative genomic, virulence, and transcriptomic analysis of emergent Streptococcus dysgalactiae subspecies equisimilis (SDSE) emm type stG62647 isolates causing human infections |
|
| Relations |
| BioSample |
SAMN41925851 |
| SRA |
SRX25218529 |
