|
| Status |
Public on Mar 09, 2021 |
| Title |
AH1263_34_C |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: AH1263
genotype: wild-type
growth medium: TSB
growth temperature: 34C
|
| Treatment protocol |
Samples were stored at -80°C prior to RNA extraction
|
| Growth protocol |
Strains were grown in TSB medium at 37°C with shaking to an OD600 of approx 6.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
total RNA, rRNA-depleted
|
| Data processing |
Raw data files (.fastq) were imported into the CLC Genomics Workbench (v11) software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped and normalized using "quantile normalization"
Normalized expression values were exported into excel files
Genome_build: The reference genome used for the analysis was based on NC_007793 and included annotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary_files_format_and_content: Expression values for each gene were initially calculated as RPKM values. The RPKM values were then normalized and the "Normalized expression values" are presented in the excel files
|
| |
|
| Submission date |
Dec 04, 2020 |
| Last update date |
Mar 09, 2021 |
| Contact name |
Ronan Kevin Carroll |
| E-mail(s) |
[email protected]
|
| Phone |
740-593-2201
|
| Organization name |
Ohio University
|
| Department |
Biological Sciences
|
| Street address |
107 Irvine Hall
|
| City |
Athens |
| State/province |
OHIO |
| ZIP/Postal code |
45701 |
| Country |
USA |
| |
|
| Platform ID |
GPL25144 |
| Series (1) |
| GSE162697 |
Staphylococcus aureus responds to physiologically relevant temperature changes by altering its global transcript and protein profile |
|
| Relations |
| BioSample |
SAMN17004446 |
| SRA |
SRX9633796 |
