|
| Status |
Public on Mar 18, 2022 |
| Title |
WT_3H_R2 |
| Sample type |
SRA |
| |
|
| Source name |
RNA cell extract
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: SH1000
timepoint: transcriptome at 3h growth
genotype/variation: wild type empty vector
|
| Treatment protocol |
no treatment
|
| Growth protocol |
After an overnight growth in TSB medium, OD measurement have been made and culture was grown 3h in TSB Cm 5 ug/mL
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lyzed with glass beads in a Fast Prep instrument and RNAs extract with Phenol/Chloroform (Trizol). Ribosomal RNAs were depleted using the Ribo-zero rRNA remmoval kit (bacteria).
NEBNext ultra directional RNA library prep kit (E7420)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
wild type empty vector replicate at 3h
|
| Data processing |
Basecalling using Illumina Native App
Reads were mapped to the S. aureus NCTC8325 genome (NC_007795.1) using CLC Genomics Workbench 11
Reads were filtered for reads properly paired and sorted by pairs
Read pairs were mapped using CLC workbench 11
Gene expression counted using CLC workbench 11
Assembly: Staphylococcus aureus subps, aureus SH1000
Supplementary files format and content: CSV file include raw counting
|
| |
|
| Submission date |
Mar 15, 2022 |
| Last update date |
Mar 19, 2022 |
| Contact name |
Liviu Cengher |
| E-mail(s) |
liviu.cengher.gr@dartmouth.edu
|
| Phone |
8583548926
|
| Organization name |
Geisel School of Medicine
|
| Department |
Microbiology and Immunology
|
| Lab |
Cheung
|
| Street address |
45 Dewey Field Rd
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
| |
|
| Platform ID |
GPL24034 |
| Series (1) |
| GSE198695 |
Regulation of spn by Teg49 in S. aureus |
|
| Relations |
| BioSample |
SAMN26677387 |
| SRA |
SRX14468431 |
