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Series GSE151570 Query DataSets for GSE151570
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.
 
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
 
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)
GSM4585923 SBW25_noplasmid_wt_AR01
GSM4585924 SBW25_noplasmid_d4242_AR02
GSM4585925 SBW25_pQBR57_wt_AR03
Relations
BioProject PRJNA636386
SRA SRP265503

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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