|
| Status |
Public on Jan 02, 2020 |
| Title |
Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence |
| Organism |
Pseudomonas aeruginosa |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Gene expression analysis of highly vs. lowly pathogenic P. aeruginosa strains identifies many virulence factors and only a few metabolism genes related to virulence. Functional transcriptomics re-analysis of core metabolism at the pathway level, reveals amino-acid, succinate, citramalate, and chorismate biosynthesis and beta-oxidation as important for full virulence and expression of these pathways indicative of virulence in various strains.
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| |
|
| Overall design |
Highly pathogenic Pseudomonas aeruginosa strains (PA14, MTB-1 and B136-33) were compared with lowly pathogenic ones (CF5, C3719 and PACS2) via RNAseq using RNA isolated from LB cultures at OD600nm 1 and 3 in 2 biological replicates each.
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| |
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| Contributor(s) |
Promponas VJ, Apidianakis Y |
| Citation(s) |
32528034 |
| |
| Submission date |
Dec 20, 2019 |
| Last update date |
Jun 14, 2020 |
| Contact name |
Vasilis J Promponas |
| E-mail(s) |
vprobon@ucy.ac.cy
|
| Organization name |
University of Cyprus
|
| Department |
Department of Biological Sciences
|
| Lab |
Bioinformatics Research Laboratory
|
| Street address |
1 Panepistimiou Avenue
|
| City |
Aglantzia |
| State/province |
Nicosia |
| ZIP/Postal code |
2109 |
| Country |
Cyprus |
| |
|
| Platforms (1) |
| GPL23385 |
Ion Torrent Proton (Pseudomonas aeruginosa) |
|
| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA597059 |
| SRA |
SRP238428 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE142464_all-ribominus.csv.gz |
273.5 Kb |
(ftp)(http) |
CSV |
| GSE142464_deseq2_B133_OD1_vs_C3719_OD1.tsv.gz |
416.8 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_B133_OD1_vs_CF5_OD1.tsv.gz |
410.4 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_B133_OD1_vs_PACS2_OD1.tsv.gz |
425.8 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_B133_OD3_vs_C3719_OD3.tsv.gz |
295.6 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_B133_OD3_vs_CF5_OD3.tsv.gz |
389.5 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_B133_OD3_vs_PACS2_OD3.tsv.gz |
385.4 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_MTB_OD1_vs_C3719_OD1.tsv.gz |
413.3 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_MTB_OD1_vs_CF5_OD1.tsv.gz |
413.4 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_MTB_OD1_vs_PACS2_OD1.tsv.gz |
422.4 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_MTB_OD3_vs_C3719_OD3.tsv.gz |
400.9 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_MTB_OD3_vs_CF5_OD3.tsv.gz |
445.0 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_MTB_OD3_vs_PACS2_OD3.tsv.gz |
434.0 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_PA14_OD1_vs_C3719_OD1.tsv.gz |
418.1 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_PA14_OD1_vs_CF5_OD1.tsv.gz |
436.6 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_PA14_OD1_vs_PACS2_OD1.tsv.gz |
433.9 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_PA14_OD3_vs_C3719_OD3.tsv.gz |
431.8 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_PA14_OD3_vs_CF5_OD3.tsv.gz |
467.8 Kb |
(ftp)(http) |
TSV |
| GSE142464_deseq2_PA14_OD3_vs_PACS2_OD3.tsv.gz |
457.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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