|
Status |
Public on Dec 10, 2022 |
Title |
SAH2 |
Sample type |
SRA |
|
|
Source name |
Bacterial
|
Organism |
Staphylococcus aureus |
Characteristics |
strain: ATCC_25923 sample groupd: SAH
|
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 |
SAH2_S32
|
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 |
SAMN19871892 |
SRA |
SRX11229407 |