Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNASeq samples of OSKM reprogrammable MEFs treated with various compounds

ABSTRACT: Examination of the impact of vitamin B12 and various one-carbon metabolism and/or epigenetic modifieres during in vitro OSKM reprogramming

ORGANISM(S): Mus musculus

PROVIDER: GSE232382 | GEO | 2023/08/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

RNASeq samples of OSKM reprogrammable MEFs treated with or without vitamin B12

Project description:Examination of the impact of vitamin B12 supplementation during in vitro OSKM reprogramming

2023-08-07 | GSE200579 | GEO

ChIPSeq of H3k36me3 samples of OSKM reprogramming mouse embryonic fibroblasts treated with B12

Project description:Examination of the impact of vitamin B12 supplementation during in vitro OSKM reprogramming on H3K36me3

2023-08-07 | GSE200578 | GEO

RNASeq samples of OSKM reprogrammable MEFs treated with various compounds

Project description:RNASeq samples of OSKM reprogrammable MEFs treated with various compounds

| PRJNA971892 | ENA

RNASeq samples of OSKM reprogrammable MEFs treated with or without vitamin B12

Project description:RNASeq samples of OSKM reprogrammable MEFs treated with or without vitamin B12

| PRJNA825467 | ENA

Vitamin B12 is a limiting factor for in vivo reprogramming

Project description:Reprogramming in vivo using OCT4, SOX2, KLF4 and MYC (OSKM) triggers cell dedifferentiation, which is considered of relevance for tissue repair and regeneration. However, little is known about the metabolic requirements of this process. We found that antibiotic depletion of the gut microbiota abolished in vivo reprogramming. Analysis of bacterial metagenomes from stool samples of wild type (WT) and OSKM mice treated with doxycycline led us to identify vitamin B12 as a key factor for in vivo reprogramming, which is partly supplied by the microbiome. We report that B12 demand increases during reprogramming due to enhanced expression of enzymes in the methionine cycle, and supplementing B12 levels both in vitro and in vivo enhances the efficiency of OSKM reprogramming.

2023-08-07 | GSE154149 | GEO

Impact of the vitamin B12 on the transcriptional regulation of the Mycobacterium tuberculosis Complex

Project description:The transcriptome in response to vitamin B12 was interrogated in three M. tuberculosis Complex species: M. tuberculosis H37Rv, M. tuberculosis GC1237, and M. bovis AF2122/97. Examination of the core B12 transcriptome resulted in a robust differential regulation of 7 genes in the three species analysed

2023-12-22 | GSE232691 | GEO

Global gene expression analysis of OSKM / N2SKM- infected MEFs over time course

Project description:We used microarrays to detail the global gene expression profiles of OSKM and N2OSKM-infected MEFs over a time course (3, 7, 11 dpi).

2010-01-22 | GSE19022 | GEO

Transcriptomic changes associated with growth of Mycobacterium tuberculosis H37Rv wild-type strain and ∆prpR mutant in mineral medium supplemented with cholesterol as the sole carbon source or standard medium supplemented with vitamin B12.

Project description:RNA-Seq results accompanying submission of a manuscript: "Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis" describing the role of cholesterol and vitamin B12 in shaping the transcriptome of the Mycobacterium tuberculosis H37Rv and M. tuberculosis ∆prpR - propionate regulator (PrpR) mutant. Next generation sequencing results are provided in three independent biological replicates for each strain growing in three different media - minimal medium with glycerol or cholesterol as the sole carbon source and standard 7H9/10% OADC medium. The influence of vitamin B12 on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium supplemented with B12. The study allowed us to re-establish the list of genes potentially involved in cholesterol metabolism. We further proposed a novel regulatory function of vitamin B12 and PrpR, a propionate regulator, in coordinated cholesterol breakdown metabolite dissipation and virulent phenotype induction. Finally, we demonstrated that a key role of cholesterol in Mtb metabolism is not only providing carbon and energy but also inducing a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment.

2021-05-31 | GSE175812 | GEO

Flexible B12 ecophysiology of Phaeocystis antarctica due to a B12-independent methionine synthase fusion protein with widespread homologues

Project description:Coastal Antarctic marine ecosystems play an important role in carbon cycling due to their highly productive seasonal phytoplankton blooms. Southern Ocean microbes are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12 ). Micronutrient limitation is a key driver of ecosystem dynamics and influences the composition of blooms, which are often dominated by either diatoms or the haptophyte Phaeocystis antarctica, each with varied impacts on carbon cycling. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remains poorly characterized. Using cultures, physiological analysis, and comparative ’omics we examined the response of P. antarctica to a matrix of Fe-B12 conditions. We show that P. antarctica is not auxotrophic for B12 , as previously suggested, and report new mechanistic insights of its B12 response in cultures of predominantly solitary and colonial cells. Proteomics coupled with proteogenomics detected a B12 -independent methionine synthase fusion protein (MetE-fusion) that is expressed under vitamin limitation and is interreplaced with the B12 -dependent isoform (MetH) in replete conditions. Database searches returned homologs of the MetE-fusion protein in multiple Phaeocystis species and in a wide range of marine microbes, including other photosynthetic eukaryotes with polymorphic life cycles and also bacterioplankton. Furthermore, MetE-fusion homologs were found to be expressed in metaproteomic and metatranscriptomic field samples in polar and more geographically widespread regions. As climate change impacts micronutrient availability in the coastal Southern Ocean, our finding that P. antarctica has a flexible B12 metabolism has implications for its relative fitness compared to B12 -auxotrophic diatoms.

2023-02-27 | PXD031524 | Pride

RRBS DNA methylation data of bovine embryonic fibroblast cells

Project description:We investigated the effects of one carbon metabolites supplementation on early embryonic development. To this end, the Bovine Embryonic Tracheal Fibroblast cell lines (EBTr; NBL-4; ATCC CCL-44) were cultured under different levels of glucose and OCM (folic acid, choline chloride, vitamin B12, and L-methionine).

2022-03-24 | GSE180362 | 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