|
| Status |
Public on Jun 25, 2019 |
| Title |
MGAS28204_ME_1 (Sample 5) |
| Sample type |
SRA |
| |
|
| Source name |
serotype M28 group A streptococcus strain
|
| Organism |
Streptococcus pyogenes |
| Characteristics |
strain: MGAS28204
sample type: clinical isolate
time point: ME
|
| Growth protocol |
Strains were grown in Todd-Hewitt broth with 0.2% yeast extract until ME (OD600 = 0.5) and ES (OD600 = 1.65) and RNAprotect was added (2:1)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Strains were lysed by ballistic disintegration and RNA extracted using Rneasy Mini Kit (Qiagen)
Libraries were prepared using standard Illumina protocols for Gram (+) organisms (clinical isolates) and standard MicrobExpress and NEB protocols for Gram (+) organisms (isogenics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Clinical_isolates_ME_v2.xlsx
clinical isolate
|
| Data processing |
Reads were mapped to the genome of serotype M28 GAS reference strain MGAS6180 using EDGEpro and differentional transcript analysis was performed with DESeq2 (version 1.14.1) using the default settings.
Genome_build: ASM1216v2 (serotype M28 GAS reference strain MGAS6180)
Supplementary_files_format_and_content: xlsx; contains RPKMs for each sample at the corresponding time point
|
| |
|
| Submission date |
Jun 24, 2019 |
| Last update date |
Jun 26, 2019 |
| Contact name |
Paul Bernard |
| E-mail(s) |
pbernard@medicine.tamhsc.edu
|
| Organization name |
Houston Methodist Research Institute
|
| Street address |
6670 Bertner Ave
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24880 |
| Series (1) |
| GSE133203 |
Polymorphisms in RocA contribute to the molecular pathogenesis of serotype M28 group A streptococcus |
|
| Relations |
| BioSample |
SAMN12125937 |
| SRA |
SRX6354126 |
