Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Compatibility of IncK plasmid lineages

ABSTRACT: Plasmids of distinct IncK lineages show a compatible phenotype

PROVIDER: PRJEB14957 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

IncK sequences

Project description:Plasmids of distinct IncK lineages show a compatible phenotype

| PRJEB15312 | ENA

A trio of bipotent precursors seeds the mesenchymal, haematopoietic, and endothelial lineages of the yolk sac

Project description:During embryogenesis, haematopoietic and endothelial lineages emerge closely in time and space. It is thought that the first blood and endothelium derive from a common clonal ancestor, the haemangioblast. However, investigation of candidate haemangioblasts in vitro has revealed a mesenchymal differentiation potential, a feature more compatible with an earlier mesodermal precursor. To date, no evidence for an in vivo haemangioblast has been discovered. Using single cell RNA-Sequencing and in vivo cellular barcoding, we have unraveled the ancestral relationships that give rise to the haematopoietic lineages of the yolk sac, the endothelium, and the mesenchyme. We show that the mesodermal derivatives of the yolk sac are produced by three distinct bipotential precursors: the haemangioblast, mesenchymoangioblast, and a novel cell type: the haematomesoblast. Between E6.5 and E7.5, this trio of precursors seeds haematopoietic, endothelial, and mesenchymal trajectories.

2022-12-21 | GSE204896 | GEO

Quantitative polyadenylation map of mouse embryonic epidermal lineages

Project description:We establish an experimental and bioinformatic pipeline using 3SEQ to quantitatively measure mRNA expression and reliably determine 3' end formation by sequencing polyadenylated transcripts. When applied to purified mouse embryonic skin stem cells direct differentiation lineages, we identify 15,651 UTRs representing 10,442 distinct mRNAs that are abundantly expressed in the skin. We determine that ~80% of UTRs are formed by using canonical A[A/U]UAAA polyadenylation signals, whereas ~20% of UTRs utilize alternative signals. We demonstrate that comparing with qPCR, our RNA-Seq approach can precisely measure mRNA fold-change and accurately determine the expression of mRNAs over four orders of magnitude. We also reported 453 out of 10,442 genes (4.3%) show differential 3' end usage between skin stem cells and their direct differentiation lineages. Among them, core components of the miRNA pathway, including Dicer, Dgcr8, Xpo5 and Ago2, show dynamic 3' UTR formation patterns, indicating a self-regulatory mechanism. Together, our quantitative analysis reveals a dynamic picture of mRNA 3' end formation in closely related somatic stem cell lineages. Perform 3SEQ in E14 epidermal basal cells and E14 epidermal suprabasal cells.

2013-01-01 | E-GEOD-37641 | biostudies-arrayexpress

Identification of distinct murine brown adipocyte lineages

Project description:Identification of distinct murine brown adipocyte lineages

| PRJNA506273 | ENA

CD161 defines a transcriptional and functional phenotype shared across distinct human T cell lineages

Project description:CD161 defines a transcriptional and functional phenotype shared across distinct human T cell lineages

| PRJNA263184 | ENA

Mycobacterium tuberculosis strain:Mtb lineages | isolate:Mtb lineages and sub-lineages

Project description:Mycobacterium tuberculosis strain:Mtb lineages | isolate:Mtb lineages and sub-lineages Genome sequencing and assembly

| PRJNA975069 | ENA

Plasmid Sequences

Project description:Plasmids isolated from the broiler caecum

| PRJEB38985 | ENA

Identification of distinct murine brown adipocyte lineages

Project description:We identify distinct murine brown adipocytes lineages using bioinformatics analysis of gene expression profiles generated by RNAseq. Further comparison with established-database for human and mouse brown fat genes enables us to sort and determine three genes to distinguish different lineages.

2019-11-01 | GSE122780 | GEO

Distinct ontogenetic lineages dictate cDC2 heterogeneity marrow of humans

Project description:Distinct ontogenetic lineages dictate cDC2 heterogeneity marrow of humans

| PRJNA1022435 | ENA

Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria

Project description:Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded IS1 elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.

2024-07-16 | GSE255663 | GEO

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