Project description:In order to study essential genomic elements in bacteria we prepare pMT85 and pMTnTetM438 mini‐transposon mutant libraries of M. pneumoniae. The dataset contains controls and the minitransposon libraries, after DNAs isolation the libraries and the controls were prepared for sequencing by HITS using standard Illumina paired‐end protocol.
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 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: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, detection of artifacts and to test different methodologies for essentiality estimation.
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.
