|
| Status |
Public on Apr 17, 2021 |
| Title |
Convergent transcriptional responses to acquisition and amelioration of different conjugative plasmids |
| Organism |
Pseudomonas [fluorescens] SBW25 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Aim: to identify the transcriptional responses to acquisition of conjugative megaplasmids by Pseudomonas fluorescens, and how these effects are impacted by known compensatory mutations. Full abstract TBC.
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| |
|
| Overall design |
Examination of effects of megaplasmid acqusition, compensatory mutations, and their combination. Ten treatments in triplicate (30 samples overall). The overall design is broadly factorial, but for some treatments design was nested. Treatments include a no-plasmid baseline control, megaplasmids alone, compensatory mutations alone (where available), and all combinations (where available).
Definitions:
dPFLU4242 is a deletion of the gene PFLU4242 (∆PFLU4242)
PQBR57_0059_V100A is a single basepair mutation in the plasmid pQBR57 causing a V100A mutation in PQBR57_0059 (T299>C)
dgacS is a deletion of the gene gacS (PFLU3777, ∆gacS)
pQBR57 is a mercury resistance plasmid (see Hall et al. 2015 doi: 10.1111/1462-2920.12901)
pQBR103 is a mercury resistance plasmid
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| |
|
| Contributor(s) |
Hall JP |
| Citation(s) |
34644303 |
| |
| Submission date |
Jun 01, 2020 |
| Last update date |
Nov 03, 2021 |
| Contact name |
James Hall |
| E-mail(s) |
j.p.j.hall@liverpool.ac.uk
|
| Organization name |
University of Liverpool
|
| Street address |
Crown Street
|
| City |
Liverpool |
| ZIP/Postal code |
L69 7ZB |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL28611 |
Illumina HiSeq 4000 (Pseudomonas fluorescens SBW25) |
|
| Samples (30)
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|
| Relations |
| BioProject |
PRJNA636386 |
| SRA |
SRP265503 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE151570_CountsMatrix.csv.gz |
356.3 Kb |
(ftp)(http) |
CSV |
| GSE151570_CountsMatrix_stats.csv.gz |
657 b |
(ftp)(http) |
CSV |
| GSE151570_de_table_chr_comp.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE151570_de_table_chr_vanc.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
| GSE151570_de_table_pQ103.csv.gz |
37.9 Kb |
(ftp)(http) |
CSV |
| GSE151570_de_table_pQ57.csv.gz |
47.8 Kb |
(ftp)(http) |
CSV |
| GSE151570_edgeR_NormalizationFactors.csv.gz |
886 b |
(ftp)(http) |
CSV |
| GSE151570_rpkm_chr.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE151570_rpkm_pQ103.csv.gz |
37.8 Kb |
(ftp)(http) |
CSV |
| GSE151570_rpkm_pQ57.csv.gz |
44.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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