|
| Status |
Public on May 01, 2017 |
| Title |
PA14 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro strains
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
description: Pseudomonas aeruginosa reference strain UCBPP-PA14
phenotype: WT
|
| Growth protocol |
Bacterial strains were grown on Mueller-Hinton broth with adjusted concentrations of Ca2+ and Mg2+ under aeration (250rpm) at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
When reached OD600=1, cells were harvested in RNA protect bacteria reagent (Qiagen) and disrupted with 2.8 mm and 0.25 mm ceramic beads in a TissueLyzer II (Qiagen) acording to manufacturer's recommendations. Total RNA was extracted using the RneasyPlus 96 kit (Qiagen), Depletion of rRNA from total RNA samples was performed with the Ribo-zero rRNA Removal reagents (Epicentre).
Libraries were constructed using the TruSeq Stranded mRNA HT Sample Prep kit (Illumina). The libraries were quantified with the Picogreen fluorescent dye and yielded around 200 to 800 ng.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped on 5892 annotated coding sequences (CDS) of PA14 using CLC Genomic Workbench 7.5 software
Transcripts abundance and differential expression results between the 3 replicates of PA14, PJ01 and PJ01ΔmexT were performed using Cuflinks and Cuffdiff algorithms
A significant difference between gene expression was considered when the q-value was less than 0.05 and when the expression ratio was between 0.3 and 3.0 folding.
Genome_build: UCBPP-PA14 accession number: NC_008463.1
Supplementary_files_format_and_content: The processed data is integrated in one only .xls file (Transcriptome CmrA + PA numbers.xls). This file contains 4 spreadsheets named: Summarized results (green tag), PA14vsPJ01, PA14vsPJ01dT and PJ01vsPJ01dT. For each gene, its homolog in the reference strain PAO1 is indicated in the column PA number. The "summarized results" sheet contains genes whose expression was found to be statistically different between the comparisons (Threshold ≥3 and ≤-3), these are the resullts presented in the Table S3 of our current manuscript. The remaining sheets (PA14vsPJ01, PA14vsPJ01dT and PJ01vsPJ01dT) contain all genes whose expression was found to be statistically different between the comparisons without any threshold.
|
| |
|
| Submission date |
Aug 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Catherine Llanes |
| E-mail(s) |
[email protected]
|
| Phone |
+330363082276
|
| Organization name |
Université de Bourgonge Franche-Comté
|
| Department |
UFR Sciences médicales et pharmaceutiques
|
| Lab |
Bactériologie
|
| Street address |
19 rue Ambroise Paré
|
| City |
Besançon |
| State/province |
Doubs |
| ZIP/Postal code |
25000 |
| Country |
France |
| |
|
| Platform ID |
GPL21297 |
| Series (1) |
| GSE86211 |
CmrA, a novel transcription regulator involved in the multidrug resistance of Pseudomonas aeruginosa |
|
| Relations |
| BioSample |
SAMN05715416 |
| SRA |
SRX2066786 |
