Project description: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 mutagenesis, and the generation of mutants via cre recombinase, catalogued via deep-sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from >50 bp to 28 Kb, which represent 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other similar regions that could not, providing a guide for future genome reductions.
Project description:We measured abundances of tRNAs by means of hydro-tRNA-seq (Gogakos et al., 2017), a method based on partial alkaline RNA hydrolysis that generates fragments suitable for sequencing, in the genome-reduced bacterium Mycoplasma pneumoniae.
Project description:To gain insight into ncRNAs functionality in bacteria, we studied the correlation of gene expression from Mycoplasma pneumoniae's ncRNAs with their overlapping ORFs over 10 different time points. This experiment contains RNAseq pair-end data from this 10 time points along Mycoplasma pneumoniae growth cycle.
Project description:To reconstruct the gene regulatory network of Mycoplasma pneumoniae, cells were treated with different drugs/perturbations or were challenged by gain or loss of function of candidate regulators, or a combination of both.
Project description:To reconstruct the gene regulatory network of Mycoplasma pneumoniae, cells were treated with different drugs/perturbations or were challenged by gain or loss of function of candidate regulators, or a combination of both.
Project description:To reconstruct the gene regulatory network of Mycoplasma pneumoniae, cells were treated with different drugs/perturbations or were challenged by gain or loss of function of candidate regulators, or a combination of both.
Project description:To reconstruct the gene regulatory network of Mycoplasma pneumoniae, cells were treated with different drugs/perturbations or were challenged by gain or loss of function of candidate regulators, or a combination of both.
Project description: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 naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from >50 bp to 28 Kb, which represent 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other similar regions that could not, providing a guide for future genome reductions.
Project description:We developed a serum and animal component-free medium capable of supporting robust growth of the genome-reduced bacterium Mycoplasma pneumoniae. Here, we performed RNA-seq expression analysis of the wild-type strain grown in serum-free vB13 medium.
