|
| Status |
Public on Jan 21, 2025 |
| Title |
Pseudomonas putida KT2440, liquid media, 6 hours, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Pseudomonas putida KT2440 |
| Characteristics |
tissue: Bacterial culture
cell type: Bacterial culture
|
| Treatment protocol |
No treatment
|
| Growth protocol |
M9 minimal media supplemented with 0.2% (v/w) citrate was used for all the experiments. When solid media was used, 1.5% (v/w) agar was added to the media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Kit (Qiagen, Venlo, Netherlands), and samples were purified from DNA using DNA‐free kit (Ambion) (Invitrogen, Carlsbad, CA, USA).
Libraries were prepared from RNA samples by the same Helmholtz Centre for Infection Research (HZI) in Braunschweig (Germany) that obtained RNASeq data.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Library name: KT2440_liquid_media_6h_replicate1
|
| Data processing |
Quality control of FASTQ files was performed using FastQC software.
Alignments were done with Bowtie 2.
HT-seq set in union mode was used to count reads per gene.
DESeq2 was used to normalize counts and set differential expression.
Fiesta was the programme that helped to build tables with the parameters of interest per gene.
Assembly: Pseudomonas putida KT2440, NCBI Reference Sequence: NC_002947.4; assembly: GCA_000007565.2 ASM756v2
Supplementary files format and content: csv files that includes comparison between liquid and solid media at 6 hours of incubation (file: SOL6hvsLIQ6h_Annotated_modif.csv).
Supplementary files format and content: csv files that includes comparison between liquid and solid media at 12 hours of incubation (file: SOL12hvsLIQ12h_Annotated_modif.csv).
Supplementary files format and content: csv files that includes comparison between liquid and solid media at 24 hours of incubation (file: SOL24hvsLIQ24h_Annotated_modif.csv).
|
| |
|
| Submission date |
Jan 17, 2025 |
| Last update date |
Jan 21, 2025 |
| Contact name |
Ángeles Hueso-Gil |
| E-mail(s) |
[email protected]
|
| Phone |
+34915854517
|
| Organization name |
Centro Nacional de Biotecnología (CNB, CSIC)
|
| Department |
Systems Biology
|
| Lab |
Environmental Microbiology
|
| Street address |
c/ Darwin 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL25301 |
| Series (1) |
| GSE287362 |
Gross transcriptomic analysis of Pseudomonas putida for diagnosing environmental shifts |
|
| Relations |
| BioSample |
SAMN46294892 |
| SRA |
SRX27388796 |
