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| Status |
Public on Jul 10, 2024 |
| Title |
Saureus_control_Rep4 |
| Sample type |
SRA |
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| Source name |
bacteria
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| Organism |
Staphylococcus aureus subsp. aureus USA300 |
| Characteristics |
cell type: bacteria
treatment: TSB medium
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| Extracted molecule |
total RNA |
| Extraction protocol |
peqGOLD Total RNA Kit, VWR Peqlab, Darmstadt, Germany
llumina® Stranded Total RNA Prep Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
mapping: bowtie2 2.4.1, default parameters
read trimming: trimmomatic 0.36, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:39
differential gene expression analysis: R 3.6.3 and DESeq2 1.26, default parameters
Assembly: ASM1467273v1, ASM1346v1
Supplementary files format and content: Table S2 RNAseq Ab in USA300 CFCM.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S3 Main RNAseq pathways Ab.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S4 RNAseq Sa in A118 CFCM.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S5 Main RNAseq pathways Sa.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: ReadCounts_AbA118_in_CFCM_and_TSB.ods
Supplementary files format and content: ReadCounts_SaUSA_in_CFCM_and_TSB.ods
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| Submission date |
Dec 14, 2023 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Manuel Wittchen |
| Organization name |
Bielefeld University
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| Department |
Center for Biotechnology
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| Street address |
Universitaetsstr. 27
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| City |
Bielefeld |
| ZIP/Postal code |
33615 |
| Country |
Germany |
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| Platform ID |
GPL29525 |
| Series (1) |
| GSE250252 |
Competitive Inhibition and Mutualistic Growth in Polymicrobial Infections: Deciphering Staphylococcus aureus – Acinetobacter baumannii Interaction Dynamics |
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| Relations |
| BioSample |
SAMN38845116 |
| SRA |
SRX22893323 |
| 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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