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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
TranscriptomicsRNASeq of multiple Mycoplasma species in wild-type condition including: Mycoplasma pneumoniae, Mycoplasma genitalium, Mycoplasma hyopneumoniae, Mycoplasma capricolum, Mycoplasma gallisepticum, Mycoplasma mycoides
The discovery of small open reading frames (smORFs) encoding for polypeptides (SEPs; <100aa) highlights that the coding capacity of the genomes has been underestimated. Most ORF-finding algorithms have historically set a minimum threshold length of 100 aa. As consequence, some transcripts encoding f...
ORGANISM(S): Mycoplasma gallisepticum str. R(high) 
2018-11-16 | E-MTAB-6203 | biostudies-arrayexpress
ProteomicsMycoplasma pneuminiae and Mycoplasma agalactiae Proteomics
During evolution, each bacterial strain shapes its metabolism in order to colonise a diversity of niches. Unraveling the biochemical reactions underlying bacteria metabolism is important for biotechnological purposes and for understanding relationships within a complex microbiome as well as the micr...
ORGANISM(S): Mycoplasma agalactiae Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2020-06-08 | PXD015800 | Pride
Mycoplamsa agalactiae Mycoplasma pneumoniae 
ProteomicsDetection of SEPs by MS - Unraveling the hidden universe of small proteins in bacterial genomes
Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is...
ORGANISM(S): Mycoplasma genitalium Mycoplasma pneumoniae Mycoplasma capricolum Mycoplasma hyopneumoniae Mycoplasma mycoides Mycoplasma gallisepticum str. R 
2019-03-01 | PXD008243 | Pride
Mycoplasma pneumoniae Mycoplasma genitalium Seps Mycoplasma mycoides. Mycoplasma gallisepticum Mycoplasma hyopneumoniae Mycoplasma capricolum 
ProteomicsDetection of SEPs by MS (Second Round)
Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is ...
ORGANISM(S): Staphylococcus aureus 
2019-10-14 | PXD011038 | Pride
Seps Staphylococcus aureus Pseudomonas aeruginosa 
ProteomicsDetection of SEPs by MS (Second Round)
Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is ...
ORGANISM(S): Escherichia coli 
2019-10-14 | PXD010490 | Pride
Seps Mycoplasma bovis Escherichia colo 
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
GenomicsTransposon random mutagenesis with MPN625 intrinsic terminator of Mycoplasma pneumoniae M129 (lab strain). 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
Transposon random mutagenesis to randomly insert the intrinsic terminator associated to the gene mpn625 from Mycoplasma pneumoniae M129. Different passage conditions (each passage equivalent to 10 cell division) are collected including 1,2,3,4,6,8, and 10 passages. This dataset is complementary to E...
ORGANISM(S): Mycoplasmoides pneumoniae 
2025-01-01 | E-MTAB-14533 | biostudies-arrayexpress
GenomicsDNASeq of different Mycoplasma pneumoniae isolated clones presenting a genomic deletion produced by a multi-recombinase engineering protocol
We developed a multi recombinase engineering rationale, that combines oligonucleotide recombineering with the selective capacity of antibiotic resistance via transient insertion of selector plasmids. We tested this method in Mycoplasma pneumoniae, a bacterium with a very inefficient native recombina...
ORGANISM(S): Mycoplasma pneumoniae M129 
2022-04-06 | E-MTAB-11600 | biostudies-arrayexpress
GenomicsBiosafety circuits for Mycoplasma - DNA-seq for passages 2, 3 and 15 of clonal Mycoplasma pneumoniae biosafety strains to study long-term stability of kill-switch devices
We have engineered synthetic gene switches to control and limit Mycoplasma growth for biosafety containment applications. Mycoplasmas have high mutation rates and, the accumulation of mutations that inactivate the circuit is expected. However, the question is how resilient is the kill-switch to muta...
ORGANISM(S): Mycoplasma pneumoniae M129 
2022-02-09 | E-MTAB-10981 | biostudies-arrayexpress
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