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| Status |
Public on Nov 22, 2019 |
| Title |
MGAS10870 (1) |
| Sample type |
SRA |
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| Source name |
MGAS10870 (1)
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| Organism |
Streptococcus pyogenes |
| Characteristics |
isolate: Parental M3 GAS isolate (MGAS10870)
growth stage: Stationary phase of growth
growth medium: THY broth growth
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| Growth protocol |
GAS strains were grown in THY broth to the stationary phase of growth (four hours after reaching an O.D.600 of 0.5)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and rRNAs were depleted using the Ribo-Zero Gram-Positive rRNA Removal Kit (Epicentre).
The rRNA depleted RNA was used to generate cDNA libraries using the ScriptSeq kit (Epicentre). Briefly, RNA was fragmented, cDNA was synthesized using random hexamers containing a 5′ tagging sequence, the RNA was hydrolyzed, and the cDNA was tagged at the 3′ end. A limited number of PCR cycles (n=12) were used to amplify the libraries via the 5′ and 3′ tags (the libraries were barcoded by using different primers), and the libraries size-selected (170 to 300 bp). The size-selected and barcoded libraries were run on an Illumina HiSeq flowcell.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
CLC Genomics Workbench version 7.5.1 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS315 genome
Parameters for alignment were set up: Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3.
Normalization was performed to overall sequencing depth using total mapped reads data.
Statistical significance was tested using Kal’s Z-test with a false-discovery rate correction.
Genome_build: ASM742v1
Supplementary_files_format_and_content: File containing columns for the gene name, Kal's Z-test with FDR correction value, normalized mean for each strain, gene start nucleotide number, gene stop nucleotide number, and expression ratios
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| Submission date |
May 15, 2019 |
| Last update date |
Nov 22, 2019 |
| Contact name |
Paul Sumby |
| Organization name |
University of Nevada
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| Department |
Microbiology & Immunology
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| Street address |
1554 N. Virginia St.
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| City |
Reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
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| Platform ID |
GPL18784 |
| Series (1) |
| GSE131239 |
Stationary phase gene regulation by the group A Streptococcus protein RocA |
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| Relations |
| BioSample |
SAMN11652423 |
| SRA |
SRX5833543 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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