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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
MetabolomicsCharacterization of Constituents with Potential Anti-Inflammatory Activity in Chinese Lonicera Species by UHPLC-HRMS Based Metabolite Profiling
This study centered on detecting potentially anti-inflammatory active constituents in ethanolic extracts of Chinese Lonicera species by taking an UHPLC-HRMS-based metabolite profiling approach. Extracts from eight different Lonicera species were subjected to both UHPLC-HRMS analysis and to pharmacol...
2022-11-17 | MTBLS3112 | MetaboLights
GenomicsTransposon sequencing to identify random insertions of lox sites in Mycoplasma pneumoniae
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 mutagen...
ORGANISM(S): Mycoplasma pneumoniae 
2021-08-18 | E-MTAB-9590 | biostudies-arrayexpress
TranscriptomicsDNA sequencing to validate random deletions in Mycoplasma pneumoniae
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 nat...
ORGANISM(S): Mycoplasma pneumoniae 
2021-08-18 | E-MTAB-9582 | biostudies-arrayexpress
UnknownAlterations in DNA Damage Response and Repair Genes as Potential Marker of Clinical Benefit From PD-1/PD-L1 Blockade in Advanced Urothelial Cancers.
Not available
S-EPMC6366295 | biostudies-literature
UnknownGenome-Wide DNA Methylation Analysis Reveals Epigenetic Dysregulation of MicroRNA-34A in TP53-Associated Cancer Susceptibility.
Not available
S-EPMC6366343 | biostudies-literature
TranscriptomicsTranscription profiling of Salmonella enterica (I) serovar Typhi Ty2 wild type and ompR null strains in a strand-specific manner
Analysis of transcriptome in a strand-specific manner to further refine previous genome annotation; RNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi ompR regulon and identify novel ompR regulated transcripts.
ORGANISM(S): Salmonella enterica 
2009-03-03 | E-TABM-644 | biostudies-arrayexpress
UnknownPharmacogenomics of the Efficacy and Safety of Colchicine in COLCOT.
Not available
S-EPMC8284376 | biostudies-literature
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
ProteomicsPHF2-mediated H3K9me balance orchestrates heterochromatin stability and progenitor proliferation in early neurogenesisPHF2-mediated H3K9me balance orchestrates heterochromatin stability and progenitor proliferation in early neurogenesis
Heterochromatin stability is crucial for progenitor proliferation during early neurogenesis. It relays on the maintenance of local hubs of H3K9me. However, the current understanding of the processes involved in the formation of efficient localized levels of H3K9me remains limited. To address this in...
ORGANISM(S): Mus musculus (Mouse) 
2024-06-11 | PXD051336 | Pride
Phf2 Dna damage Neural stem cells Heterochromatin integrity Histone demethylation 
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