|
| Status |
Public on Mar 11, 2024 |
| Title |
E1_derived |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
cell type: bacterial cells
background strain: PAO1
genotype: derived from delta_crcZ; FAA resistant
|
| Growth protocol |
Samples were obtained by centrifugation (7000 rpm, 20 min, 4 °C) of a bacterial culture in exponential phase in LB medium (OD600 ≈ 0.6). The sediment was kept at ‐80 °C until processing, for a maximum of 1 month.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysozyme was added to this pellet to a final concentration of 1 mg/ml. It was incubated for 10 min at room temperature with intermittent vortexing. Sonication was performed for 3 intermittent cycles of 20 s (0.4 power) followed by incubation periods at 4 °C. RNA extraction continued with the commercial RNA easy minikit (QIAGEN) system. DNA was removed using the RNase-Free DNAse Set (QIAGEN), and possible DNA debris with the Turbo DNA-free system (AMBION). DNA contamination was ruled out by PCR with the rplU gene primers. Ribosomal RNA was removed with the Ribo‐Zero Magnetic Kit Bacteria system (Epicentre).
The library was prepared using 3.5 μg of treated RNA, with the TruSeq RNA sample preparation kit v2 system (Illumina).
The RNA-seq experiment was performed at the Antonia Martín Gallardo Genomics Unit, Parque Científico de Madrid, with the Genome Analyzer IIx (Illumina) in a single reading format (1x75 nt).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
E1_derived
|
| Data processing |
The quality of the sequences obtained was analyzed using the FastQC program.
Read alignment and quantification was performed using Rockhopper (PMID: 23716638).
Assembly: Assembly genome ASM676v1 (NCBI Reference Sequence: NC_002516.2).
Supplementary files format and content: Pseudorevertants_expression.txt is a tab-separated file containing the raw counts corresponding all (11) samples analized. Gene identifiers columns are: Name=gene name; Synonym=Uniprot Primary Accession; Product=Product description in NCBI Protein.
|
| |
|
| Submission date |
Feb 16, 2023 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Rafael Torres |
| E-mail(s) |
rafael.torres@cnb.csic.es
|
| Organization name |
CNB
|
| Department |
Bioinformatics for Genomics and Proteomics (BioinfoGP)
|
| Lab |
Bioinformatics for Genomics and Proteomics (BioinfoGP)
|
| Street address |
Darwin 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15987 |
| Series (1) |
| GSE225437 |
Analysis of ΔcrcZ suppressor mutations |
|
| Relations |
| BioSample |
SAMN33269506 |
| SRA |
SRX19350798 |
