|
| Status |
Public on Dec 10, 2022 |
| Title |
SA2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: ATCC_25923
sample groupd: SA
|
| Growth protocol |
Cell were grown and treated as described in the attached article
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated as describe in attached article
Standard library preparation protocol as describe in attached article
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SA2_S30
|
| Data processing |
mapping of reads was done using: bowtie2 --local using Escherichia coli K12 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
Count values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Escherichia coli ASM74325v1, NCBI_Assembly:GCA_000743255.1
Genome_build: Staphylococcus aureus ASM75620v1, NCBI_Assembly:GCA_000756205.1
Supplementary_files_format_and_content: Tab delimited text file
|
| |
|
| Submission date |
Jun 25, 2021 |
| Last update date |
Dec 10, 2022 |
| Contact name |
Anne de Jong |
| E-mail(s) |
anne.de.jong@rug.nl
|
| Phone |
+31 50 363 2047
|
| Organization name |
university of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17452 |
| Series (1) |
| GSE178890 |
G-quadruplex DNA as a target for pathogenic bacteria: efficacy of an extended naphthalene diimide ligand and mode of action |
|
| Relations |
| BioSample |
SAMN19871894 |
| SRA |
SRX11229405 |
