Phenome analysis of Mycoplasma pneumoniae
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB10038 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To discover new gene functions in Mycoplasma pneumoniae, cells were treated with different drugs/perturbations.
2016-04-01 | E-MTAB-3771 | biostudies-arrayexpress
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.
2016-04-01 | E-MTAB-3772 | biostudies-arrayexpress
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.
2016-04-01 | E-MTAB-3773 | biostudies-arrayexpress
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.
2019-07-31 | E-MTAB-4642 | biostudies-arrayexpress
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.
2019-07-31 | E-MTAB-6229 | biostudies-arrayexpress
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.
2015-07-09 | E-MTAB-3076 | biostudies-arrayexpress
Project description:Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. We have found 68 new non-annotated transcripts, of which the vast majority are potential regulatory RNAs, 53 of them in antisense to known genes. Integration of all data confirmed a dynamic and complex view of bacterial transcription: Under reference conditions in a rich medium, 138 polycistronic and 212 monocistronic transcripts could be identified, with almost half of the polycistronic operons showing a ‘staircase’-like expression pattern, i.e. the expression level within each gene is constant, but succeeding genes have lower expression. Furthermore, under different conditions, operons can divide into smaller transcriptional units, possibly by utilization of internal promoters resulting in many alternative transcripts. More complex bacteria show similar responses to external stresses, although M. pneumoniae lacks the respective transcription regulators, indicating the existence of yet uncharacterized common response mechanisms. This is supported by the concerted expression of genes, some of which with common upstream DNA motifs, form distinct operons under different conditions indicating additional factors regulating their expression. Frequent antisense transcripts, alternative transcripts and multiple regulators per gene thus cannot longer be seen as indicators of eukaryote-specific regulatory complexity. Keywords: stress response, time series
2009-12-11 | GSE14014 | GEO
Project description:Mycoplasma pneumoniae is a model organism for the minimal cell, so tit is believe to have the basic transcriptional machinery. To reconstruct its gene regulatory network, cells were treated with different drugs/perturbations or were challenged by gain or loss of function of candidate transcription factos and regulators, or a combination of both and RNAseq was performed. Perturbations allow to link the upstream signals and the putative regulators.
2019-07-31 | E-MTAB-4784 | biostudies-arrayexpress
Project description:Mycoplasma pneumoniae is a model organism for the minimal cell, so tit is believe to have the basic transcriptional machinery. To reconstruct its gene regulatory network, cells were treated with different drugs/perturbations or were challenged by gain or loss of function of candidate transcription factors and regulators, or a combination of both and RNAseq was performed. Perturbations allow to link the upstream signals and the putative regulators.
2019-07-31 | E-MTAB-7153 | biostudies-arrayexpress
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.
2021-08-18 | E-MTAB-9590 | biostudies-arrayexpress