Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In-vitro human gut microbiota culture with added sugars

ABSTRACT: Three human gut microbiome samples from different individuals were cultured in an optimized culture medium with or without the presence of different sugars (10 mM glucose, 20 mM fructose, 10 mM glucose + 20 mM fructose, or 10 mM kestose). Samples were cultured in technical triplicates, and were taken at 0 hr, 1hr, 5 hr, 12 hr and 24 hr of culturing for optical density and metaproteomic analyses. Cultured microbiota cells were subjected to metaproteomics analysis using LC-MS/MS and a TMT approach.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Human Gut Metagenome

SUBMITTER: Zhibin Ning

LAB HEAD: Daniel Figeys

PROVIDER: PXD037925 | Pride | 2024-06-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Leyuan_20211211_Exploris_Niche_study_AllMixQC_1.raw	Raw
	Leyuan_20211211_Exploris_Niche_study_AllMixQC_2.raw	Raw
	Leyuan_20211211_Exploris_Niche_study_AllMixQC_3.raw	Raw
	Leyuan_20211211_Exploris_Niche_study_V46_A.raw	Raw
	Leyuan_20211211_Exploris_Niche_study_V46_B.raw	Raw

Items per page:

1 - 5 of 26

Publications

Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes.

Wang Tong T Li Leyuan L Figeys Daniel D Liu Yang-Yu YY

ISME communications 20240101 1

The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundanc ...[more]

PMID: 38808120

Similar Datasets

Isotope Tracing Analysis in Intestinal Organoids with fructose

Project description:We isolated and cultured Intestinal Organoids from Mouse. To trace the metabolism of fructose, intestinal organoids were cultured in unlabeled fructose-containing DMEM/F12 medium (10 mM D-fructose, 0 mM D-glucose, 2.5 mM L-glutamine) for 12 hr, and then switched into 13C labeled fructose-containing medium (10 mM U-[13C] D-fructose, Sigma-aldrich) for 6 hr.

2020-12-09 | ST001622 | MetabolomicsWorkbench

Transcriptomic data of MDA-MB-231 cells adapted to culture in media containing different sugars (glucose or fructose) and cultured as mammospheres

Project description:We report the single-cell RNA sequencing data obtained from MDA-MB-231 breast cancer cells cultured in standard DMEM with 25 mM glucose, or adapted to culture in DMEM with 10 mM fructose to reduce glycolysis, and then cultured as mammospheres

2018-05-22 | GSE106202 | GEO

Transcriptomic data of MCF7 cells adapted to culture in media containing different sugars (glucose or fructose) and cultured in 2D on plastic

Project description:We report the single-cell RNA sequencing data obtained from MCF7 breast cancer cells cultured in standard DMEM with 25 mM glucose, or adapted to culture in DMEM with 10 mM fructose to reduce glycolysis, and cultures in 2D on plastic

2020-05-28 | GSE115869 | GEO

Effect of restricted glycolysis on gene expression in MDA-MB-231 cells

Project description:Cultured breast cancer cells in standard media are highly glycolytic To determine the effect of glycolysis on gene expression in MDA-MB-231 we adapted cells to cuture in mediae containing 10 mM fructose, and compared the gene expression to cells cutured in standard high glucse (25 mM) DMEM

2021-02-01 | GSE111204 | GEO

Effect of restricted glycolysis on gene expression in MCF-7 cells

Project description:Cultured breast cancer cells in standard media are highly glycolytic To determine the effect of glycolysis on gene expression in MCF-7 we adapted cells to cuture in mediae containing 10 mM fructose, and compared the gene expression to cells cutured in standard high glucose (25 mM) DMEM

2021-02-01 | GSE110960 | GEO

Untargeted metabolomics of intestinal organoids treated with fructose

Project description:We performed untargeted metabolomics of intestinal organoids treated with fructose (10 mM) for 24 hr.At the 5th day of secondary organoid culture, the organoids were treated with fructose (10 mM D-fructose)-containing IntestiCult organoid growth medium for 24 hr and washed with pre-cooled PBS before harvesting.

2020-12-09 | ST001621 | MetabolomicsWorkbench

Specific serum methylome of the serrated pathway of colorectal carcinogenesis

Project description:This study was conducted to explore the serum methylome of precancerous lesions belonging to the serrated pathway of colorectal carcinogenesis in a prospective multicentre cohort. Individuals were grouped into five main categories: (i) serrated adenocarcinoma (SAC), (ii) high-risk serrated polyps (HR-SP) comprising traditional serrated adenomas (TSA), sessile serrated lesions (SSL), and serrated polyps (SP) with dysplasia or ≥ 10 mm; (iii) high-risk hyperplastic polyps (HR-HP), defined as HP ≥ 10 mm; (iv) low-risk serrated lesions (LR-SL) including SP without dysplasia < 10 mm and HP < 10 mm; and (v) healthy individuals with no colorectal findings (NCF). First, epigenome-wide methylation levels were quantified in pooled cfDNA samples to characterize the differential methylation profile between no serrated neoplasia (NSN: NCF and LR-SL) and high-risk serrated lesions (HR-SL: HR-HP and HR-SP); concordance with tissue methylation levels was assessed using external datasets. Then, the pathway-specific cfDNA methylation signature was evaluated together with cfDNA pools from the conventional CRC pathway. cfDNA was extracted from serum samples and methylation measurements were assessed with the Infinium MethylationEPIC BeadChip. Data was mainly preprocessed and analyzed with R/Bioconductor packages.

2024-03-01 | GSE199173 | GEO

STING mediates lupus via the activation of conventional dendritic cell maturation and plasmacytoid dendritic cell differentiation

Project description:BMDCs from WT, Fcgr2b-/- and Stinggt/gt were cultured, then stimulated with DMXAA for 3 and 6 hr. Cells were collected and lysed with 1 % IGEPAL CA-630, 0.5% TritonX-100, 150 mM NaCl, 50 mM Tris pH 7.4, 5% glycerol, 100 mM beta-Glycerophosphate, 2 mM Na3VO4 and 1X proteases inhibitor cocktail (Roche). First, antibody were mixed with the magnetic beads by adding 10 µg of STING antibody with 400 ug of SureBeads™ Protein A magnetic beads (Biorad, California, USA) and incubated for 1 hour at room temperature. Then, Protein lysates were added and incubated with antibody-conjugated beads for overnight at 4oC. After incubation, the beads were washed 3 times with wash buffer (150 mM NaCl and 50 mM Tris-HCL pH 7.4). Samples were eluted by adding 5X laemmli buffer and, boiled 950C for 10 minutes. The eluted protein samples were separated by 10 % SDS-PAGE gel. The STING interacting proteins from co-IP were analyzed by in-gel digestion followed by LC-MS/MS analysis.

2020-09-14 | PXD019239 | Pride

The gene expression profiles of hypoxia-resistant (HR) human multiple myeloma cell lines

Project description:In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, RPMI8226-HR derived from RPMI8226 cells, KMS-11-HR derived from KMS-11, U266-HR derived from U266, and IM-9-HR derived from IM-9 cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used RPMI8226 cells and RPMI8226-HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from RPMI8226 cells (normoxia or hypoxia) and exosomes derived from RPMI8226-HR cells (hypoxia-resistant, HR sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the RPMI8226-HR cells significantly increased tube formation of HUVECs than those from RPMI8226 cells.

2018-02-06 | GSE110113 | GEO

E. coli TG1/pBS(Kan)Synhox and pBS(Kan) hydrogen production

Project description:E. coli TG1 with pBS(Kan)Synhox can produce more hydrogen than TG1/pBS(Kan). To reveal the difference of metabolic activity (gene expression) between these strains in producing hydrogen, the differential gene expression analyses were performed. All samples cultured in complex medium with fructose containg 5 mM IPTG. Keywords: hydrogen production

2007-08-13 | GSE5905 | 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