|
| Status |
Public on Apr 17, 2023 |
| Title |
ST40_biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
N315
|
| Organism |
Staphylococcus aureus |
| Characteristics |
cell line: N315
genotype: N315ex w/oPhi deltacomK1
|
| Growth protocol |
Cultures of S. aureus were grown in CS2 medium, at 37°C and 180 rpm until the OD600 reached 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To quench cellular metabolism / transcription and to stabilize RNAs, cells were harvested by centrifugation at 10,000 g for 1 min at 4°C and the pellets immediately frozen in liquid nitrogen before storage at −80°C.
For extraction of RNA, cells were lysed using Lysing Matrix B and a FastPrep instrument (both MP Biomedicals), and RNA were isolated using the RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Total RNA Stranded Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
bcl2fastq2-2.18.12
Sequence reads were trimmed for adaptor sequence using Cutadapt 1.15
Trimmed sequence reads were mapped to Staphylococcus aureus subsp. Aureus N315 using bwa 0.6.2-r126
Read count were performed using FeaturesCount from subread-1.5.2 package (parameters : -s 2 (Perform reversely-stranded read counting), -t gene)
Differential analysis using DESeq2 1.28.1
Assembly: Staphylococcus aureus subsp. Aureus N315, GenBank : BA000018.3
Supplementary files format and content: tab-delimited csv files include count for each sample
|
| |
|
| Submission date |
Feb 09, 2023 |
| Last update date |
Apr 18, 2023 |
| Contact name |
Nicolas Mirouze |
| E-mail(s) |
nicolas.mirouze@i2bc.paris-saclay.fr
|
| Organization name |
Institute for the Integrative Biology of the Cell
|
| Street address |
Avenue de la Terrasse
|
| City |
GIF SUR YVETTE |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL28116 |
| Series (1) |
| GSE224932 |
Characterization of SigH, ComK1 and ComK2 regulons during competence development in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN33226383 |
| SRA |
SRX19321982 |
