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TranscriptomicsTransposon random mutagenesis of Mycoplasma pneumoniae M129. Samples sequenced for passage numbers 1, 2, 3, 4, 6, 8 and 10, two biological replicates per passage and two technical replicates for passages 2-4.
Controlled dataset covering multiple passage conditions, from the genome-reduced bacterium Mycoplasma pneumoniae, to test and validate two new software tools: FASTQINS and ANUBIS. These computational tools allow the generation of insertion profile datasets from raw transposon sequencing data, detect...
ORGANISM(S): Mycoplasma pneumoniae M129 
2020-08-28 | E-MTAB-8918 | biostudies-arrayexpress
ProteomicsEngineered live bacteria suppress Pseudomonas aeruginosa lung infection in mouse and dissolve biofilm in endotracheal tubes from patients
Engineered live bacteria could provide a new modality for treating lung infections , a major cause of mortality worldwide. Here, we engineered a genome-reduced human lung bacterium, Mycoplasma pneumoniae, to treat ventilator-associated pneumonia (VAP), a disease with high hospital mortality when ass...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2023-10-24 | PXD037233 | Pride
Engineered live bacteria  pseudomonas aeruginosa  lung infection  mouse  biofilm  endotracheal tubes 
GenomicsTransposon sequencing to identify random insertions of lox sites in Mycoplasma pneumoniae
This dataset was used to assess the random insertion by tranposases of lox sites in Mycoplasma pneumoniae. This is part of the protocol LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of Lox sites by transposon mutagen...
ORGANISM(S): Mycoplasma pneumoniae 
2021-08-18 | E-MTAB-9590 | biostudies-arrayexpress
TranscriptomicsDNA sequencing to validate random deletions in Mycoplasma pneumoniae
We present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of Lox sites by transposon mutagenesis, and the generation of mutants via cre recombinase, catalogued via deep-sequencing. When LoxTnSeq was applied to the nat...
ORGANISM(S): Mycoplasma pneumoniae 
2021-08-18 | E-MTAB-9582 | biostudies-arrayexpress
ModelsWodke2013 - Genome-scale constraint-based model of M.pneumoniae energy metabolism (iJW145)
Wodke2013 - Genome-scale constraint-based model of M.pneumoniae energy metabolism (iJW145) A new genome-scale metabolic reconstruction of M.pneumoniae is used in combination with external metabolite measurement and protein abundance measurements to quantitatively explore the energ...
2005-01-01 | MODEL1301290000 | BioModels
ModelsLlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case2
LlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case1 Three putative effects of the asRNAs were considered in this study: in case 1 , the binding of the asRNA to the corresponding mRNA induces degradation of the duplex. In case 2   (this model)   the binding o...
2017-05-18 | MODEL1511170001 | BioModels
ModelsLlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case1
LlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case1 Three putative effects of the asRNAs were considered in this study: in case 1  (this model) , the binding of the asRNA to the corresponding mRNA induces degradation of the duplex. In case 2, the binding of the ...
2017-05-18 | MODEL1511170000 | BioModels
ModelsLlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case3
LlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case3 Three putative effects of the asRNAs were considered in this study: in case 1, the binding of the asRNA to the corresponding mRNA induces degradation of the duplex. In case 2, the binding of the asRNA to...
2017-05-18 | MODEL1511170002 | BioModels
GenomicsTransposon random mutagenesis of Mycoplasma pneumoniae M129 using ProTInSeq protocol along different concentrations and using two positive selection markers (Chloramphenicol acetyltransferase and Erythromycin esterase EreA) and a negative selection marker (barnase)
Definition of different Tn4001-derived mini-transposons carrying reporters with no translation initiation codons so they can only be expressed when fused to an endogenous protein. We used Chloramphenicol acetyltransferase (Cm) as a positive selection marker while the RNAse barnase (Barn) was used as...
ORGANISM(S): Mycoplasma pneumoniae M129 
2023-07-31 | E-MTAB-10380 | biostudies-arrayexpress
TranscriptomicsRNA-seq differential expression analysis of tmRNA (ssrA) mutants in the genome-reduced bacterium Mycoplasma pneumoniae
We used a combination of genetic and proteomic approaches to characterize tmRNA (ssrA) activity in the genome-reduced bacterium Mycoplasma pneumoniae. For this, we generated tmRNA mutants encoding a tag resistant to proteolysis. Endogenous protein tagging by the mutant tmRNA gene (ssrAmk) was then e...
ORGANISM(S): Mycoplasma pneumoniae 
2021-08-09 | E-MTAB-10111 | biostudies-arrayexpress
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