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| Status |
Public on Nov 20, 2023 |
| Title |
LAC_wt_rep1 |
| Sample type |
SRA |
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| Source name |
bacterial
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| Organism |
Staphylococcus aureus |
| Characteristics |
cell type: bacterial
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a RNeasy Mini Kit with the following modifications. Cells were lysed by incubation with 100 mM TRIS-HCL with 800 ng/µl lysostaphin for 25 min at 37 °C. Subsequently, 700 µl RLT buffer containing β-mercaptoethanol were added and samples were transferred to lysing matrix B tubes and the samples were subjected to three bead beating steps (30 sec x 3; 1 min on ice in between). RNA was treated with turbo DNAse kit according to manufacturers instructions.
Depletion of ribosomal RNA and library preparations were performed at the Genomics Core at the University of Colorado Anschutz Medical Campus using the Illumina Ribo-ZeroTm Plus rRNA depletion kit and the Zymo-Seq RiboFree total RNA library 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 |
Qiagen CLC Genomics Workbench v 20.0.4
Raw sequencing reads in fastq format were imported, adapter sequences trimmed and the reads were mapped to the USA300 FPR3757 reference genome using Qiagen CLC Genomics Workbench with default settings.
Trim settings: Automatic removal of read-through adapter sequences. Removal of low quality sequence (limit = 0.05).
Trimmed sequence reads were mapped to NC_007793 using CLC Genomics Workbench (Mapping settings: mismatch cost: 2 insertion cost: 3, deletion cost: 3, length fraction: 0.8 similarity fraction: 0.8)
Read count extraction was performed using CLC Genomics Workbench.
Assembly: NC_007793
Supplementary files format and content: tab-deliminated text file for each sample
Supplementary files format and content: tab-deliminated text files contain information regarding gene name, chromosome, region, expression value, TPM, RPKM, gene length, unique gene reads and total gene reads
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| Submission date |
Jul 31, 2023 |
| Last update date |
Nov 20, 2023 |
| Contact name |
Katrin Schilcher |
| E-mail(s) |
ks665@leicester.ac.uk
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| Organization name |
University of Leicester
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| Department |
Genetics and Genome Biology
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| Street address |
University Road
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| City |
Leicester |
| State/province |
Leicestershire |
| ZIP/Postal code |
LE1 7RH |
| Country |
United Kingdom |
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| Platform ID |
GPL27158 |
| Series (1) |
| GSE239718 |
The Staphylococcus aureus CamS lipoprotein is a repressor of toxin production that shapes host-pathogen interaction |
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| Relations |
| BioSample |
SAMN36776095 |
| SRA |
SRX21202512 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7670360_1_4_S4_L004_R1_001_wt.txt.gz |
88.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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