|
| Status |
Public on May 16, 2023 |
| Title |
K279a_STAT_Biol_Replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Stenotrophomonas maltophilia K279a |
| Characteristics |
tissue: Bacterial culture
strain: K279a
growth phase: stationary growth phase
|
| Treatment protocol |
Quorum sensing conditions were created either by growing cells to stationary phase or by adding the autoinducers DSF or AHL.
|
| Growth protocol |
All bacterial cultures were done in LB at 37C in a shaking incubator at 200 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy Mini Kit (Qiagen).
TruSeqTM Stranded Total RNA kit protocol (Illumina Inc.) was used to construct the stranded total RNA-Seq libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GIBERT_01_new_annot_wo_outlier_STAT_vs_LOG_results.xlsx
GIBERT_01_new_annot_wo_outlier_STAT_vs_LOG_norm_counts.txt
|
| Data processing |
Sequence mapping was perfomed with STAR/2.5.3a
Quantification with RSEM/1.3.0
The differential gene expression analysis was performed using the DESeq2 R package using an adjusted p-value < 0.05 (FDR of 5%) as a cut-off for statistical significance, with the Benjamini-Hochberg correction for multiple testing
Assembly: Stenotrophomonas maltophilia K279a NC_010943.1 (2017)
Supplementary files format and content: excel files include Fold change and p-values for each compared condition
|
| |
|
| Submission date |
Jun 20, 2022 |
| Last update date |
May 16, 2023 |
| Contact name |
Isidre Gibert |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitat Autònoma de Barcelona (UAB)
|
| Department |
Institut de Biotecnologia i de Biomedicina (IBB)
|
| Lab |
Bacterial Molecular Genetics
|
| Street address |
Carrer de la Vinya, s/n
|
| City |
Bellaterra |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL32370 |
| Series (1) |
| GSE206442 |
Transcriptome analysis of S. maltophilia in the exponential and stationary phases and after a treatment with quorum sensing autoinducers. |
|
| Relations |
| BioSample |
SAMN29205654 |
| SRA |
SRX15797122 |
