Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mycoplasma pneumoniae transposon libraries

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mycoplasma pneumoniae M129

SUBMITTER: Javier Delgado

PROVIDER: E-MTAB-3075 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes

Project description:This sample was prepared with a modified version of the Tn4001 transposon commonly used in Mycoplasmas. This transposon is described to work more efficiently in Mycoplasma agalactiae and, by extension, in other Mycoplasma species. This sample was prepared transforming this bacteria with a newly designed transposon named pMTnGm-SynMyco to test its efficiency by Transposon Sequencing tracked by deep sequencing.

2019-11-15 | E-MTAB-7425 | biostudies-arrayexpress

Transcription factor-SNP interactome for colorectal cancer risk loci

Project description:A core task to understand the consequences of non-coding single nucleotide polymorphisms (SNP) is to identify their genotype specific binding of transcription factor (TF). Here, we generate a large-scale TF-SNP interaction map for a selection of 116 colorectal cancer (CRC) risk loci and validated TF binding to 10 putatively functional SNPs. Our data further revealed TF binding complexity adjacent to the 116 risk loci, adding an additional layer of understanding to regulatory networks associated with CRC relevant loci.

2017-02-23 | PXD004435 | Pride

Genome wide analysis of genes involved in efflux function and regulation within Escherichia coli and Salmonella enterica serovar Typhimurium

Project description:Expression of efflux pumps is a key feature of most cells which are resistant to multiple antibiotics. This study used TraDIS-Xpress, a genome wide transposon mutagenesis technology to identify genes in Escherichia coli and Salmonella Typhimurium involved in drug efflux and its regulation. We exposed mutant libraries to the canonical efflux substrate acriflavine in the presence and absence of the efflux inhibitor phenylalanine-arginine β-naphthylamide. Comparisons between conditions identified efflux specific and drug specific responses. Known efflux associated genes were easily identified including: AcrAB-TolC, MarA, RamA and SoxS confirming specificity of the response. Further genes encoding cell envelope maintenance enzymes and products involved with stringent response activation, DNA housekeeping, respiration and glutathione biosynthesis were also identified as affecting efflux activity in both species. We identified a conserved set of pathways crucial for efflux activity in these experimental conditions which expands the list of genes known to impact efflux efficacy.

2022-11-12 | E-MTAB-12353 | biostudies-arrayexpress

High-throughput sequencing analysis of the relative frequency of Contacts between Sister Copies emerging from a replication fork in Vibrio cholerae

Project description:Paired-end deep-sequencing was used to determine in parallel the status and position of sister-chromatid contact (SC2) reporters and/or site-specific recombinase (SSR) activity reporters inserted at random positions in a library of cells. The SC2 reporters are short recombination cassettes for a topology-independent site-specific recombinase (Cre or Xer). The SSR-activity reporters are long recombination cassettes. The SC2 reporter cassettes are composed of two directly-repeated recombination sites separated by a DNA segment too short to permit their excision by intramolecular recombination. The SSR-activity cassettes are composed of two directly-repeated recombination sites separated by a DNA segment long enough to permit their excision by intramolecular recombination. The assays start with the engineering of a cell line with a conditional expression allele for Cre or Xer and the creation of a library of cells harbouring a cognate SC2 or SSR-activity reporter at different genomic positions. Production of the recombinase was induced for different lengths of time during cell growth and/or at specific stages of the cell cycle. The position of the SC2 reporter harboured by each cell and the recombination status of the recombination cassette it contains are then determined by high-throughput paired-end sequencing.

2020-07-07 | E-MTAB-8946 | biostudies-arrayexpress

Amplicon-based targeted re-sequencing analysis of target genes in human DNA samples using the Illumina TruSeq Custom Amplicon technology

Project description:Amplicon-based targeted re-sequencing analysis was performed in the patient-derived gliobastoma cell culture samples. For this purpose, genomic DNA (gDNA) was isolated and DNA libraries were prepared using the TruSeq Custom Amplicon Low Input (Illumina, Inc.) technology. By this, a pool of 375 amplicons was generated for each single sample in order to enrich for the target genes ATRX1, EGFR, IDH1, NF1, PDGFRA, PIK3CG, PIK3R1, PTEN, RB1 and TP53. Sequencing was performed on the Illumina MiSeq® next generation sequencing system (Illumina Inc.) and its 2 x 250 bp paired-end v2 read chemistry. The resulting reads were quality controlled and mapped against the human reference genome (hg19). For all samples, sequence variations of the amplified regions of interest in comparison to the human reference sequence were identified and filtered based on reliability.

2021-07-07 | E-MTAB-9343 | biostudies-arrayexpress

Extracellular ATP elicits DORN1-mediated RBOHD phosphorylation to regulate stomatal aperture

Project description:A multibillion dollar pharmaceutical industry targets purinergic signaling pathways in humans. However, in contrast, little is known about purinergic signaling in plants. Extracellular adenosine-5’-triphosphate (eATP) acts as a damage-associated molecular pattern (DAMP) in both animals and plants. The first plant eATP receptor, DORN1, was identified in Arabidopsis, defining a new kinase family (P2K) of purinoceptors. Stomates are leaf pores that control gas exchange and, therefore, impact critical functions such as photosynthesis and drought tolerance. Stomates are also the prefer entry point for leaf pathogens. The addition of ATP led to the rapid closure of Arabidopsis leaf stomates resulting in enhanced resistance to the bacterial pathogen Psuedomonas syringae. The data indicate that this response is mediated by eATP recognition by DORN1 followed by direct phosphorylation of the NADPH oxidase RBOHD, resulting in elevated production of reactive oxygen species and stomatal closure. Mutation of the DORN1 phosphorylation sites on RBOHD eliminated the ability of eATP to induce stomatal closure. To date, in contrast to work in animals, purinergic signaling in plants has been viewed as a curiosity without any direct, mechanistic connection to key plant processes. The data presented clearly demonstrates eATP as an important signal controlling stomatal aperture with important implications for the control of plant photosynthesis, water homeostasis, pathogen resistance and ultimately yield.

2018-10-24 | PXD006678 | Pride

Transposon 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)

Project description: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 a negative one. In this case, the mini-transposon has a constitutively expressed chloramphenicol resistance gene downstream to the Barn gene. Also, Erythromycin esterase EreA (Ery) was used to evaluate the effect of oligomerization of protein-fusion resistances, as Ery is a dimeric resistance while Cm forms a tetramer. In the positive selection, for the bacteria to survive in the presence of Chloramphenicol, the transposed reporter needs to be inserted in-frame to a genome protein-coding sequence. In the negative selection, the transposed gene should be out of frame with the genome protein-coding sequence for the bacteria to survive.

2023-07-31 | E-MTAB-10380 | biostudies-arrayexpress

Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Pattern

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-29 | E-GEOD-51764 | biostudies-arrayexpress

Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Patterns [BS-Seq]

Project description:A forward genetics screen led to the identification of the putative chromatin regulator EDM2 as a cellular anti-silencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite PHD finger domain that recognizes both active H3K4 and repressive H3K9 methylation marks at the intronic repeat elements in genes such as the histone H3K9 demethylase gene IBM1, and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes.Our results thus increase the understanding of anti-silencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin. Col-0 and edm2-4 total genomic DNAs are extracted from leaves and then subjected to bisulfite convertion and sequencing in accordance with standard protocol.

2013-10-29 | E-GEOD-51762 | biostudies-arrayexpress

The characteristics of genome-wide DNA methylation in naM-CM-/ve CD4+ T cells of patients with psoriasis and atopic dermatitis

Project description:Psoriasis and atopic dermatitis (AD) are characterized by polarized CD4+ T cell responses. During the polarization of naM-CM-/ve CD4+ T cells, DNA methylation plays an important role in the regulation of gene transcription. In this study, we profiled the genome-wide DNA methylation status of naM-CM-/ve CD4+ T cells in patients with psoriasis or AD and healthy controls using a ChIP-seq method. As a result, twenty-six regions in the genome ranging in size from 10 to 70 kb were markedly hypomethylated in patients with psoriasis. These regions were mostly pericentromeric on 10 different chromosomes and overlapped with various strong epigenomic signals, such as histone modifications and transcription factor binding sites, that were observed in the ENCODE project. Gene-centric analysis indicated that the promoter regions of 124 genes on the X chromosome had dramatically elevated methylation levels in patients with psoriasis as compared to those from healthy controls (> 4-fold). Moreover, immune-related genes on the X chromosome had higher hypermethylation than other genes (P < 0.05). These findings imply that methylation changes in naM-CM-/ve CD4+ T cells may affect CD4+ T cell polarization, especially in the pathogenesis of psoriasis. Keywords: Psoriasis, Atopic dermatitis, DNA methylation, naM-CM-/ve CD4+ T cells Sample submission examines DNA methylation from human naive CD4+ T cells in patients with psoriasis and atopic dermatitis. Note: Raw data available only for Sample GSM871288.

2012-03-17 | E-GEOD-35582 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data