Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiles of neonatal intestinal organoids under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention

ABSTRACT: Transcriptome profiles of neonatal intestinal organoids under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention

PROVIDER: PRJNA1175033 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR31047635_1.fastq.gz	Fastqsanger.gz
	SRR31047635_2.fastq.gz	Fastqsanger.gz
	SRR31047636_1.fastq.gz	Fastqsanger.gz
	SRR31047636_2.fastq.gz	Fastqsanger.gz
	SRR31047637_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Transcriptome profiles of RAW264.7 cells under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention

Project description:Transcriptome profiles of RAW264.7 cells under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention

| PRJNA1172333 | ENA

Transcriptome profiles of neonatal intestinal organoids under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention

Project description:We performed RNA sequencing to identify the role of fibroblast in the effects of tryptphan metabolites on LPS-stimulated mouse neonatal intestinal organoids.

2025-05-13 | GSE279881 | GEO

Transcriptome profiles of neonatal mouse intestinal organoids with or without LPS sitimulation and tryptophan metabolites intervention

Project description:Transcriptome profiles of neonatal mouse intestinal organoids with or without LPS sitimulation and tryptophan metabolites intervention

| PRJNA1175034 | ENA

Transcriptome profiles of RAW264.7 cells under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention

Project description:We performed RNA sequencing to identify the role of fibroblast in the effects of tryptphan metabolites on LPS-stimulated RAW264.7 cells.

2025-05-13 | GSE279383 | GEO

Transcriptome profiles of neonatal mouse intestinal organoids with or without LPS sitimulation and tryptophan metabolites intervention

Project description:We performed RNA sequencing to identify the effects of tryptphan metabolites on LPS-stimulated intestinal fibroblast.

2025-05-13 | GSE279880 | GEO

SIRT6 regulates Tryptophan catabolism preventing metabolite imbalance and neurodegeneration

Project description:In the brain, tryptophan byproducts are involved in the biosynthesis of proteins, energy-rich molecules (e.g., NAD+), and neurotransmitters (serotonin and melatonin). Impaired tryptophan catabolism, seen in aging, neurodegeneration and psychiatric diseases affects mood, learning, and sleep; however, the reasons for those impairments in elder and these ailments remain unknown. Our results from cellular, Drosophila melanogaster, and mouse models indicate that SIRT6 regulates tryptophan catabolism by balancing its usage. Mechanistically, SIRT6 regulates tryptophan and sleep quality through changes in gene expression of key genes (e.g., TDO2, AANAT), which results in elevated concentration of neurotoxic metabolites from the kynurenic pathway at the expense of serotonin and melatonin production. Such neurotoxic metabolites can affect various processes in the brain. However, by redirecting tryptophan through TDO2 inhibition in our new SIRT6-KO Drosophila model, the impairments in neuromotor behavior and vacuolar formation a parameters of neurodegeneration could be significantly reversed.

2025-10-01 | GSE309387 | GEO

Intervention with metabolites emulating endogenous cell transitions accelerates muscle regeneration in young and aged mice

Project description:Tissue regeneration following an injury requires dynamic cell-state transitions that allow for establishing the cell identities required for the restoration of tissue homeostasis and function. Here, we present a biochemical intervention that induces an intermediate cell state mirroring a transition identified during normal differentiation of myoblasts and other multipotent and pluripotent cells to mature cells. When applied in somatic differentiated cells, the intervention, composed of one-carbon metabolites, reduces some dedifferentiation markers without losing the lineage identity, thus inducing limited reprogramming into a more flexible cell state. Moreover, the intervention enabled accelerated repair after muscle injury in young and aged mice. Overall, our study uncovers a conserved biochemical transitional phase that enhances cellular plasticity in vivo and hints at potential and scalable biochemical interventions of use in regenerative medicine and rejuvenation interventions that may be more tractable than genetic ones.

2024-01-23 | GSE145933 | GEO

Changes in tryptophan de novo NAD synthesis associated with chronic intestinal inflammation

Project description:Tryptophan metabolism and de novo NAD biosynthesis is associated with behavioural changes in IBD patients. The microbiota and tryptophan de novo syntheses of the distal colon, distal colon and brain of C57BL/6 control mice and Winnie mice littermates with chronic intestinal inflammation were compared using RNA-Seq. Differentially expressed genes were analysed using Micromon software. Changes in tryptophan and nicotinamide metabolism-associated gene expressions, metabolites, and abundance of gut microbiota associated with chronic intestinal inflammation and dysregulated tryptophan metabolism in the Winnie mouse distal colon and brain were apparent. Our findings shed light on the physiological alterations in tryptophan metabolism, specifically its diversion from the serotonergic pathway towards the kynurenine pathway and the consequential effects on de novo NAD+ synthesis, in the context of chronic intestinal inflammation

2024-06-28 | GSE264317 | GEO

prokaryote coculture

Project description:prokaryote coculture overview

| PRJNA1028757 | ENA

Tryptophan plays a central role in yeast’s tolerance to isobutanol

Project description:Isobutanol is considered a potential biofuel and can be produced by genetically modified microorganisms. Saccharomyces cerevisiae inherently produces isobutanol through valine intermediate(s), so it serves as a good host. However, isobutanol's toxicity remains a key obstacle for bioproduction. In our study, we first used image recognition to screen the colony growth of a yeast gene deletion library and inferred that genes involved in tryptophan biosynthesis, ubiquitination, and the pentose phosphate pathway (PPP) contribute to isobutanol tolerance. The importance of tryptophan in yeast's tolerance to isobutanol was confirmed by the recovery of isobutanol tolerance in a tryptophan biosynthesis defective strain by adding exogenous tryptophan. Transcriptomic analysis revealed that amino acid biosynthesis- and transportation-related genes in a tryptophan biosynthesis defective host were up regulated under conditions such as nitrogen starvation. This may explain why ubiquitination for protein degradation was involved for the protein turnover. PPP metabolites and vitamin B1/B6 may serve as precursors and cofactors in tryptophan biosynthesis to enhance isobutanol tolerance. Furthermore, the tolerance mechanism may also be linked to tryptophan metabolism, including the kynurenine pathway and nicotinamide adenine dinucleotide biosynthesis. Both pathways are responsible for cellular redox balance and antioxidative ability and figured out that tryptophan may play a crucial role on isobutanol tolerance. Our study highlights the central role of tryptophan in yeast's isobutanol tolerance and offers new clues for engineering a yeast host with strong isobutanol tolerance.

2021-10-20 | GSE175794 | 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