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GenomicsDNA-seq of an ELMSeq reporter cassette to study impact of C-terminal sequence variations on protein abundance
A ELMSeq reporter cassette was created to monitor Dam levels by methylation, and introduced in the genome. The regions of 6 nt upstream and 6 nt downstream the stop codon were randomized to study their effect on gene expression. The ELMSeq reporter cassette was composed of: promoter - dam - random N...
ORGANISM(S): Mycoplasma pneumoniae 
2020-05-04 | E-MTAB-8223 | biostudies-arrayexpress
GenomicsDNA-seq of ELMSeq reporter cassette
A ELMSeq reporter cassette was created to monitor Dam levels by methylation, and introduced in the genome. Some regions upstream dam were randomized to see their effect on gene expression. So the cassette consists in: 4xGATC sites - (promoter) - random region - dam. The amplicon was spanning the who...
ORGANISM(S): Mycoplasma pneumoniae 
2017-11-08 | E-MTAB-5365 | biostudies-arrayexpress
TranscriptomicsDam-specific RNA-seq
To determine the transcription start site and the abundance of dam mRNA, we conducted mRNA-specific RNA-Seq experiments. Essentially two strategies were tested. First strategy: We obtained the cDNA with a specific RT-PCR in order to get the mRNA from our dam construct (see DNA-seq of DamID reporter...
ORGANISM(S): Mycoplasma pneumoniae 
2018-03-22 | E-MTAB-5363 | biostudies-arrayexpress
ProteomicsELM-seq - A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants
Quantitative analysis of the sequence determinants of transcription and translation regulation is of special relevance for systems and synthetic biology applications. Here, we developed a novel generic approach for the fast and efficient analysis of these determinants in vivo. ELM-seq (expression le...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2017-08-29 | PXD005606 | Pride
Screening Transcription Reporter Translation 
GenomicsProtein occupancy of Mycoplasma pneumoniae chromosome
Protein occupancy is a means of identifying all the regions in the genome that are bound to proteins. A simple protocol is used whereby cross-linked chromatin is digested with DNase to remove all non-crosslinked, naked, DNA. To distinguish the regions that are bound by RNA polymerase from the rest, ...
ORGANISM(S): Mycoplasma pneumoniae M129 
2016-04-01 | E-MTAB-3783 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of Mycoplasma pneumoniae II
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.
ORGANISM(S): Mycoplasma pneumoniae M129 
2016-04-01 | E-MTAB-3773 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of Mycoplasma pneumoniae I
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.
ORGANISM(S): Mycoplasma pneumoniae M129 
2016-04-01 | E-MTAB-3772 | biostudies-arrayexpress
TranscriptomicsPhenome analysis of Mycoplasma pneumoniae
To discover new gene functions in Mycoplasma pneumoniae, cells were treated with different drugs/perturbations.
ORGANISM(S): Mycoplasma pneumoniae M129 
2016-04-01 | E-MTAB-3771 | biostudies-arrayexpress
ProteomicsMycoplasma pneumoniae Gene Regulatory Network VII
Determining the gene regulatory network of an organism is fundamental to achieving a global understanding of cell behavior. In general, studies of transcription regulation are limited to the annotated transcription factors, not considering other non-canonical regulators. Here we describe the first s...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2019-11-12 | PXD007565 | Pride
Systems biology Transcription factor Bacteria Minimal cell Microbiology Gene expression Proteome Regulation 
ProteomicsDNA Affinity chromatografy on Mycoplasma pneumoniae extracts I
Determining the gene regulatory network of an organism is fundamental to achieving a global understanding of cell behavior. In general, studies of transcription regulation are limited to the annotated transcription factors, not considering other non-canonical regulators. Here we describe the first s...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2019-11-12 | PXD007674 | Pride
Mycoplasma pneumoniae System biology Transcription factor Affinity chromatography Minimal cell Microbiology Gene expression Dna binding protein Proteome Regulation 
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