|
| Status |
Public on Aug 27, 2019 |
| Title |
GAS-delmtsR-100um-manganese-OD1-0-rep-2 |
| Sample type |
SRA |
| |
|
| Source name |
cell pellet
|
| Organism |
Streptococcus pyogenes |
| Characteristics |
serotype: MGAS10870
tag: invasive infection isolate
growth phase: Late-exponential (LE, OD600nm=1.0)
|
| Treatment protocol |
at the desired growth stage, late-exponential 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 Ribo-Zero (Epicentre)
resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Epicentre)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
multiplexed SE libraries were sequenced on an Illumina HiSeq 2500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-Seq reads from strain MGAS10870 were mapped to reference strain MGAS315 (GenBank accession number AE014074.1) using Edge-pro v1.3.1(Estimated Degree of Gene Expression for Prokaryotes).
mapping reads from each strain to respective refrence using Edge-pro v1.3.1 yields raw and normalized (RPKM) expression values for each gene.
varible gene content and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
differential expression analysis was perfomed using DESeq2 v1.6.3 runing in R version 3.1.3. Raw reads were used as the input and normalized expression generated using DESeq2's default normalization method Relative log expression (RLE) approcah was used to generate fold change values for each gene. Multiple testing correction was performed using Benjamini-Hochberg method.
|
| |
|
| Submission date |
Mar 19, 2019 |
| Last update date |
Aug 27, 2019 |
| Contact name |
Muthiah Kumaraswami |
| E-mail(s) |
mkumaraswami@houstonmethodist.org
|
| Organization name |
Houston Methodist Research Institute
|
| Department |
Infectious Diseases
|
| Street address |
6670 Bertner Ave
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL20656 |
| Series (1) |
| GSE128534 |
Global gene expression analysis of MGAS10870 serotype of Group A Streptococcus (Streptococcus pyogenes/GAS) in the absence or presence of 100 µM Manganese |
|
| Relations |
| BioSample |
SAMN11166297 |
| SRA |
SRX5543170 |
