|
| Status |
Public on Aug 24, 2015 |
| Title |
10870::rocAM1 |
| Sample type |
SRA |
| |
|
| Source name |
Enriched mRNA
|
| Organism |
Streptococcus pyogenes |
| Characteristics |
strains: Complementation strain
genotype description: M3 rocA gene replaced with M1 rocA gene in M3 background
genotype: RocA+
|
| Growth protocol |
All GAS strains were grown to an O.D.600 of 0.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
GAS cultures were incubated with RNAprotect™ (Qiagen) for >5 min at room temperature, pelleted and frozen at -80 °C overnight. Cells were resuspended in RLT-BME and lysed using FastPrep Lysing Matrix B tubes (MP Biomedicals) in FastPrep-24 machine. Samples were processed twice at speed 4 for 15 sec. Total RNA was then isolated using miRNEasy Mini Kit (Qiagen) and eluted in nuclease-free water. Off-column DNase treatments, using DNA-free DNase (Ambion), was performed at 37 °C. The mRNA was then enriched using Ribo-Zero rRNA Removal Kit (Bacteria) to deplete rRNA contamination.
All cDNA libraries were constructed using ScriptSeq™ RNA-Seq Library Preparation Kit (Epicentre) and processed according to manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
CLC Genomics Workbench version 7.5.1 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS315 genome (AE014174.1). Parameters for alignment were set up: Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3, and Deletion cost=3. Normalization of the data was accomplished using the Kal's Z-test with FDR from the total read count.
Genome_build: AE014174.1
Supplementary_files_format_and_content: Excel files containing all coding regions from genome with raw and normalized expression values, RPKM, coding region nucleotide start and stop, Kal's Z-test calculations, and raw and normalized means. The normalized means were used for calcuating transcript fold change between samples.
|
| |
|
| Submission date |
Apr 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric W Miller |
| E-mail(s) |
ericmiller@medicine.nevada.edu
|
| Organization name |
University of Nevada Reno
|
| Department |
Microbiology and Immunology
|
| Street address |
1664 N Virginia St
|
| City |
Reno |
| State/province |
Nevada |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL19982 |
| Series (1) |
| GSE68277 |
Regulatory Rewiring Confers Serotype-Specific Hyper-Virulence in the Human Pathogen Group A Streptococcus |
|
| Relations |
| BioSample |
SAMN03568906 |
| SRA |
SRX1010049 |
