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Status |
Public on Mar 23, 2022 |
Title |
Newman 2 min rep 1 |
Sample type |
SRA |
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Source name |
Staphylococcus aureus Newman growing exponentionally in MPB infected with phage K
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Organism |
Staphylococcus aureus |
Characteristics |
strain: Newman infection: Staphylococcus virus K time: 2 min
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Growth protocol |
MPB exponential growth
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Extracted molecule |
total RNA |
Extraction protocol |
The total RNA was extracted using organic extraction with TRIzol. Genomic DNA was removed using a Turbo DNA-free kit. The rrRNA depletion was performed using a RiboMinus Bacteria 2.0 Transcriptome Isolation Kit according to the manufacturer’s instructions. Sequencing libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina kit, following the standard protocol.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
N2DESeq2_res.csv
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Data processing |
Raw reads quality control with FastQC Quality trimming and filtering performed using Trimmomatic toolkit (v 0.36) with the following parameters: ILLUMINACLIP:TruSeq3-SE:2:30:10 SLIDINGWINDOW:4:15 LEADING:22 TRAILING:22 MINLEN:20 AVGQUAL:22 Alignment to the reference genome and read counting using using STAR v 2.5.2b with the following parameters: outFilterMultimapScoreRange 0, outFilterMatchNmin 30, outFilterMatchNminOverLread, 0.95, outFilterMismatchNmax 999, outFilterMismatchNoverLmax 0.02, outFilterMismatchNoverReadLmax 1, alignIntronMin 20, alignIntronMax 1 Normalization of counts within the triplicates and DGE analysis was performed with DESeq2 package Genome_build: Staphylococcus aureus SH1000 de novo sequenced genome (Bioproject Accession: PRJNA769253), Staphylococcus aureus Newman (Genbank Accession: NC_009641.1), Staphylococcus virus K (GenBank Accession: NC_005880.2 ) Supplementary_files_format_and_content: csv file with raw counts generated using aligner STAR for each sample Supplementary_files_format_and_content: csv file with normalized counts generated using DESeq2 for each sample Supplementary_files_format_and_content: csv file with DESeq2 results for each sampling time
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Submission date |
Dec 10, 2021 |
Last update date |
Mar 23, 2022 |
Contact name |
Adela Finstrlova |
E-mail(s) |
indrakova.a@gmail.com
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Organization name |
Masaryk University
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Department |
Department of Experimental Biology
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Lab |
Laboratory of Molecular Diagnostics of Microorganisms
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Street address |
Kamenice 5
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City |
Brno |
ZIP/Postal code |
62500 |
Country |
Czech Republic |
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Platform ID |
GPL24034 |
Series (1) |
GSE190637 |
Global transcriptomic analysis of bacteriophage-host interactions between Kayvirus therapeutic phage and Staphylococcus aureus |
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Relations |
BioSample |
SAMN23849065 |
SRA |
SRX13376852 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5726915_N2A_STARcounts.csv.gz |
13.4 Kb |
(ftp)(http) |
CSV |
GSM5726915_N2A_normCounts.csv.gz |
24.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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