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| Status |
Public on Jun 27, 2023 |
| Title |
SAUSA300_0903 [S18] |
| Sample type |
SRA |
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| Source name |
SAUSA300_0903
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| Organism |
Staphylococcus aureus |
| Characteristics |
strain background: USA300 (JE2)
genotype/variation: Mutant in SAUSA300_0903
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| Growth protocol |
Grown in LB broth up to 1.0 (OD600)
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| Extracted molecule |
total RNA |
| Extraction protocol |
6 hypothetical mutants (SAUSA300_1720, SAUSA300_1902, SAUSA300_1650, SAUSA300_2068, SAUSA300_0903 and SAUSA300_0917 ) were grown in LB broth up to 1.0 (OD600nm). Bacterial RNA was extracted by using the RNA kit (E.Z.N.A. Total RNA kit I) after a brief lysostaphin step.
RNA libraries were prepared on 8ug of total RNA. rRNA was removed using the Ribo-zero kit. mRNA was fragmented and cDNA synthesized using random hexamers, after which custom second-strand synthesis buffer (Illumina), dNTPS, Rnase H and DNA polymerase I were added to intiate the second-strand synthesis. A series of terminal repair, ligation and sequencing adaptor ligation, the double-stranded cDNA library is size selection and PCR enriched.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
S18
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| Data processing |
Analysis was performed using Partek Flow
Reads were trimmed with Phred scores <20, 20bp minimum length and a maximum N of 10%, along with adaptor sequences removed
Trimmed reads were aligned using Bowtie 2
Combined alignments were quantified to the annotation model
Filtered counts were normalized by using TMM and adding 1 then excluding feature less than 1
Differential analysis was conducted using ANOVA and Limma-voom
Genome_build: GCA_000013465.1_ASM1346v1_cds_from_genomic
Supplementary_files_format_and_content: xlsx
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| Submission date |
Aug 28, 2019 |
| Last update date |
Jun 27, 2023 |
| Contact name |
Dane Parker |
| E-mail(s) |
[email protected]
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| Phone |
9739723047
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| Organization name |
Rutgers New Jersey Medical School
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| Department |
Pathology, Immunology and Laboratory Medicine
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| Street address |
205 South Organge Ave, G-1208
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| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07103 |
| Country |
USA |
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| Platform ID |
GPL27158 |
| Series (1) |
| GSE136543 |
Characterized functions of hypothetical genes identified by Tn-seq important for pathgoenesis of Staphylococcus aureus pneumonia |
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| Relations |
| BioSample |
SAMN12647177 |
| SRA |
SRX6777838 |
| 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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