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| Status |
Public on Jun 20, 2023 |
| Title |
YF13 isolate 3 |
| Sample type |
SRA |
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| Source name |
YF13
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| Organism |
Staphylococcus aureus |
| Characteristics |
cell line: YF13
genotype: LAC agr KO
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| Treatment protocol |
Not treateted
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| Growth protocol |
Grown in Tryptic Soy Broth media with shaking (180rpm), at 37 C, for 5 h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were spun down, treated with ice-cold Trizol and homogenized by bead beating using Lysing Matrix B tubes. Upon centerifugation and treatment with chloroform and isopropanol, aquos phase was transferred to RNeasy spin column, washed, and eluted to DEPC treated water.
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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 |
Raw reads were mapped to the Staphylococcus aureus LAC genome assembly GCF_015475575.1 using Bowtie2.
featureCounts was used to generate a read count table.
Assembly: GCF_015475575.1
Supplementary files format and content: gene_counts.tsv - tab separated table of read counts per gene
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| Submission date |
Jun 24, 2022 |
| Last update date |
Jun 20, 2023 |
| Contact name |
Gregory Putzel |
| Organization name |
NYU Langone Health
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| Department |
Microbiology
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| Lab |
Pironti
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| Street address |
430 East 29th Street
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL27158 |
| Series (2) |
| GSE206889 |
The quorum-sensing agr system protects Staphylococcus aureus from oxidative stress (5 hour growth) |
| GSE207045 |
The quorum-sensing agr system protects Staphylococcus aureus from oxidative stress |
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| Relations |
| BioSample |
SAMN29333975 |
| SRA |
SRX15890116 |
| 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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