 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 23, 2022 |
| Title |
Newman 20 min rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Staphylococcus aureus Newman growing exponentionally in MPB infected with phage K
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: Newman
infection: Staphylococcus virus K
time: 20 min
|
| Growth protocol |
MPB exponential growth
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
N20DESeq2_res.csv
|
| 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
|
| |
|
| Submission date |
Dec 10, 2021 |
| Last update date |
Mar 23, 2022 |
| Contact name |
Adela Finstrlova |
| E-mail(s) |
indrakova.a@gmail.com
|
| Organization name |
Masaryk University
|
| Department |
Department of Experimental Biology
|
| Lab |
Laboratory of Molecular Diagnostics of Microorganisms
|
| Street address |
Kamenice 5
|
| City |
Brno |
| ZIP/Postal code |
62500 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL24034 |
| Series (1) |
| GSE190637 |
Global transcriptomic analysis of bacteriophage-host interactions between Kayvirus therapeutic phage and Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN23849048 |
| SRA |
SRX13376862 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5726925_N20B_STARcounts.csv.gz |
12.9 Kb |
(ftp)(http) |
CSV |
| GSM5726925_N20B_normCounts.csv.gz |
21.8 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 |
|
|
|
|
 |
