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| Status |
Public on May 30, 2022 |
| Title |
Control 30 min R1 |
| Sample type |
SRA |
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| Source name |
Control 30 min
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| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: Z154
strain type: mucoid strain from CF
cell type: planktonic cells
growth phase: mid-exponential phase
treatment: untreated (control)
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| Treatment protocol |
The cells were challenged with or without NAC 8000 mg/L for 30 minutes at 35°C in static conditions. All experiments were carried out in 2 biological replicates.
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| Growth protocol |
Overnight cultures in cation-adjusted Mueller-Hinton broth of P. aeruginosa Z154 were diluted 1:50 into 40 mL of the same medium (appropriately concentrated in order to avoid broth dilution when NAC solution were used), and incubated at 35°C in agitation to achieve OD600 = 1.0. 5 mL of the cells at mid-exponential phase (OD600 = 1.0) were moved into 2 wells of a multiwell plate prior to treatment.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the SV Total RNA Isolation System (Promega, Madison, WI, USA) with minor modifications. Briefly, 1 mL of each culture was transferred to sterile tubes and cells harvested by centrifugation (12,000 xg for 10 minutes) at 5°C. The cell pellet was resuspended in 100 µL of 0.4 mg/mL lysozyme in TE buffer and incubated at room temperature for 5 minutes. RNA was purified according to the manufacturer’s RNA purification by centrifugation protocol, including a second elution step performed with 50 μL of nuclease-free water. The purified RNA was then stored at –70°C prior to ribosomal RNA depletion and sequencing. Total RNA quantity and quality, ribosomal RNA (rRNA) depletion, cDNA library construction and Illumina HiSeq 4000 platform-based RNA-sequencing were performed by Eurofins Genomics Europe Sequencing (Constance, Germany).
The transcriptome libraries were strand-specific and single-end sequenced with 50-bp reads, for a total of 10 million reads per sample. At least 20 ng of rRNA-depleted RNA was used as input.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Bioinformatic analysis was performed using the SeqMan NGen v17.3 software tool (DNASTAR Lasergene, Madison, WI, USA), with default parameters.
There are two sequencing files (fastq.gz) for the second biological replicate in order to achieve the guaranteed number of reads. For downstream analysis, we used both files and we grouped them as the same replicate for each sample.
Reads were aligned using P. aeruginosa Z154 complete genome (n=6,344 CDSs) as reference (GenBank accession number CP069177).
DESeq2 was selected as RNA-Seq normalization method.
Differentially expressed genes (DEGs) of the NAC-exposed cultures compared to control were analyzed considering false discovery rate (FDR) adjusted p-values of <0.05 from DESeq2.
Genome_build: GenBank accession number CP069177.
Supplementary_files_format_and_content: text files containing raw counts and normalized abundance measurements from DESeq2 of sequencing reads per replicate per sample.
Supplementary_files_format_and_content: text file containing all the processed results for each feature type and each sample (i.e., raw counts, linear rlog reads, p-value, adjusted p-value, log2 fold-change).
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| Submission date |
Dec 15, 2021 |
| Last update date |
Jun 03, 2022 |
| Contact name |
Felice Valzano |
| E-mail(s) |
felice.valzano@unisi.it
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| Organization name |
University of Siena
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| Department |
Medical Biotechnologies
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| Lab |
FiBiM Lab
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| Street address |
Viale Mario Bracci, 16
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| City |
Siena |
| State/province |
Siena |
| ZIP/Postal code |
53100 |
| Country |
Italy |
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| Platform ID |
GPL24583 |
| Series (1) |
| GSE190946 |
Transcriptomic response of Pseudomonas aeruginosa Z154 planktonic cultures to N-acetylcysteine exposure. |
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| Relations |
| BioSample |
SAMN24060560 |
| SRA |
SRX13439059 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5736065_control_30min_R1.txt.gz |
391.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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