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

db8aebfb-a32b-4b69-b8ac-ba2d83f2b599 - samples

Project description:46 human stool sample metagenomes as matched controls having no direct occupational links with farming of slaughter. Samples were derived from the LifeLines cohort from the Northern parts of the Netherlands. http:///www.lifelines.nl.

| EGAD00001005443 | EGA

Diagnosis of Taenia solium infections based on “mail order” RNA-sequencing of single tapeworm egg isolates from stool samples

Project description:Combined community health programs aiming at health education, preventive antiparasitic chemotherapy, and vaccination of pigs have proven their potential to regionally reduce and even eliminate Taenia solium infections that are associated with a high risk of neurological disease through ingestion of T. solium eggs. Yet it remains challenging to target T. solium endemic regions precisely or to make exact diagnoses in individual patients. One major reason is that the widely available stool microscopy may identify Taenia ssp. eggs in stool samples as such, but fails to distinguish between invasive (T. solium) and less invasive Taenia (T. saginata, T. asiatica, and T. hydatigena) species. The identification of Taenia ssp. eggs in routine stool samples often prompts a time-consuming and frequently unsuccessful epidemiologic workup in remote villages far away from a diagnostic laboratory. Here we present “mail order” single egg RNA-sequencing, a new method allowing the identification of the exact Taenia ssp. based on a few eggs found in routine diagnostic stool samples. We provide first T. solium transcriptome data, which show extremely high mitochondrial DNA (mtDNA) transcript counts that can be used for subspecies identification. “Mail order” RNA-sequencing can be administered by health personnel equipped with basic laboratory tools such as a microscope, a Bunsen burner, and access to an international post office for shipment of samples to a next generation sequencing facility. Our suggested workflow combines traditional stool microscopy, RNA-extraction from single Taenia eggs with mitochondrial RNA-sequencing, followed by bioinformatic processing with a basic laptop computer. The workflow could help to better target preventive healthcare measures and improve diagnostic specificity in individual patients based on incidental findings of Taenia ssp. eggs in diagnostic laboratories with limited resources.

2021-11-06 | GSE175668 | GEO

Discovery of a Novel Human Polyomavirus in Acute Diarrheal Samples from Children

Project description:By unbiased deep sequencing, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. From Mexico, 12 samples (out of 96) were positive for MxPyV by MXPyV-specific PCR. We used the ViroChip microarray and PCR to screen these 12 samples for co-infection with common diarrheal viruses. Six of 12 MxPyV-positive diarrheal samples tested negative by the ViroChip and PCR, and the other 6 samples were positive for at least one known diarrheal virus.

2012-10-01 | GSE40008 | GEO

NCL_CS_Neonates

Project description:Preterm Neonatal Stool Metagenomes

| PRJEB49383 | ENA

DNA methylation analysis in malignant melanoma clinical samples [450K array]

Project description:Comprehensive DNA methylation analysis in malignant melanoma clinical samples. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 54 malignant melanoma cases and primary melanocyte culture.

2020-10-22 | GSE140169 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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