|
| Status |
Public on Apr 24, 2020 |
| Title |
SVAR_STR1_RPMI_2 |
| Sample type |
SRA |
| |
|
| Source name |
STR1_RPMI+10%LB_no vancomycin
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: TCH1516
gentotype/variation: STR1
culture media: RPMI+10%LB
treatment: no vancomycin
|
| Treatment protocol |
cultures were treated with 0.5x MIC of vancomycin
|
| Growth protocol |
The strains were grown in each respective media, with and without vancomycin (at 1/2 MIC). At OD 0.2, cultures without vancomycin were harvested. At the same OD, cultures were treated with 0.5x MIC of vancomycin, and harvested for RNA 30min after. Harvesting of the cells consisted in mixing of 3 mL of culture with two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m.. The supernatant was decanted, and the cell pellet was stored at −80 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Quick RNA Fungal/Bacterial Microprep (Zymo Research), following vendor procedures, including an on-column DNase treatment. RNA quality and purity was assessed using Nanodrop and Bioanalyzer RNA nano chip. Ribosomal RNA was removed from total RNA preparations using RNaseH.
RNA was used to build a cDNA library for sequencing using a KAPA Stranded RNA-seq Library Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
UO1_HRS_SVAR_STR1_RPMI_2_S32
|
| Data processing |
The phred quality scores for the Illumina sequencing reads were generated using FastQC package
Bowtie2 was used to align the raw reads to TCH1516 genome (GCA_000017085.1) and to calculate alignment percentage
The aligned reads were then normalized to transcripts per million (TPM) with DESeq2
Genome_build: GCA_000017085.1
Supplementary_files_format_and_content: csv file with deseq2 TPM values for all samples
|
| |
|
| Submission date |
Apr 23, 2020 |
| Last update date |
Apr 24, 2020 |
| Contact name |
Henrique Machado |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California San Diego
|
| Department |
Bioengineering
|
| Lab |
Systems Biology Research Group
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL25144 |
| Series (1) |
| GSE149213 |
Transcriptional landscape changes after tolerization adaptive laboratory evolution of Staphylococcus aureus to vancomycin |
|
| Relations |
| BioSample |
SAMN14680043 |
| SRA |
SRX8164291 |
