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Sample GSM8391987 Query DataSets for GSM8391987
Status Public on Jul 20, 2024
Title RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35904_rep2
Sample type SRA
 
Source name MGCS35904
Organism Streptococcus dysgalactiae subsp. equisimilis
Characteristics tissue: MGCS35904
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 SAMN41925859
SRA SRX25218537

Supplementary file Size Download File type/resource
GSM8391987_MGCS35904_rep2.rpkm.txt.gz 42.2 Kb (ftp)(http) TXT
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Raw data are available in SRA

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