Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS ENHANCED DETECTION AND ANNOTATION OF SMALL MOLECULES IN METABOLOMICS USING MOLECULAR NETWORK-ORIENTED PARAMETER OPTIMIZATION

ABSTRACT: Both BerriHealth Premium Alcohol Free Black Raspberry Extract (BRB liquid) and Freeze-Dried Black Raspberry Powder (BRB powder) were purchased from Berrihealth company (Oregon, US). Abbreviation: L: liquid; P: powder; R: resolution; I: intensity; N: NCE; E: exclusion time.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Rubus Occidentalis (ncbitaxon:75079)

SUBMITTER: Jiangjiang Zhu

PROVIDER: MSV000087069 | GNPS | Thu Mar 18 09:24:00 GMT 2021

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

An Ancient COI1-independent Function for Reactive Electrophilic Oxylipins in Thermotolerance [seq]

Project description:Algal discs were transferred to a 12-well plate containing 2 ml liquid 0.5 Gamborg’s B5 mock or OPDA 25 µM, incubated for 2 hours on a shaker (120 rpm) and then the algae were frozen in liquid nitrogen and ground to a fine powder.

2020-03-04 | GSE141417 | GEO

Avian pathogenic Escherichia coli infection causes infiltration of heterophilic granulocytes of chick tracheal by the complement and coagulation cascades pathway

Project description:Tracheal mucosal epithelial cells were scraped at 12 and 24 hours of infection, frozen in liquid nitrogen and stored at -80°C. The cells were sent to a biotechnology company for TMT quantitative proteomic analysis. The cells were sent to a biotech company for TMT quantitative proteomics analysis.

2024-01-26 | PXD044411 | Pride

Comparative proteomic analysis of Bacillus subtilis and Aspergillus niger in Black Soldier Fly co-fermentation

Project description:the original data of black soldier fly larva mass fermentation with Bacillus subtilis and Aspergillus niger, analyzed by Chinese biotechnology company, published by Chinese Academy of Tropical Agricultural Sciences Environment and Plant Protection Institute for research only.

2023-10-25 | PXD037713 | JPOST Repository

Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs.

Project description:Long noncoding RNA (lncRNA) transcripts have emerging impacts in cancer studies, which suggests their potential as novel therapeutic agents. However, the molecular mechanism behind their treatment effects is still unclear. Here, we designed a computational model to Associate LncRNAs with Anti-Cancer Drugs (ALACD) based on a bilevel optimization model, which optimized the gene signature overlap in the upper level and imputed the missing lncRNA-gene association in the lower level. ALACD predicts genes coexpressed with lncRNAs mean while matching drug's gene signatures. This model allows us to borrow the target gene information of small molecules to understand the mechanisms of action of lncRNAs and their roles in cancer. The ALACD model was systematically applied to the 10 cancer types in The Cancer Genome Atlas (TCGA) that had matched lncRNA and mRNA expression data. Cancer type-specific lncRNAs and associated drugs were identified. These lncRNAs show significantly different expression levels in cancer patients. Follow-up functional and molecular pathway analysis suggest the gene signatures bridging drugs and lncRNAs are closely related to cancer development. Importantly, patient survival information and evidence from the literature suggest that the lncRNAs and drug-lncRNA associations identified by the ALACD model can provide an alternative choice for cancer targeting treatment and potential cancer pognostic biomarkers. The ALACD model is freely available at https://github.com/wangyc82/ALACD-v1.

| S-EPMC6948815 | biostudies-literature

Degradome analysis in Phalaenopsis aphrodite subsp. formosana

Project description:We performed one degradome sequencing for identification and characterization of novel microRNAs in Phalaenopsis aphrodite subsp. formosana. Plant tissues of leaves, stalk, and flower buds frozen in liquid nitrogen were ground to fine powder using a mortar and pestle, respectively. Total RNA extraction was freshly prepared using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. About 50 μg of leaves with or without low temperature treatment, stalks and flower buds were taken separately and then mixed. The degradome library was constructed by the Genomics BioSci & Tech. Company following the manufactoring protocol. In brief, 200 μg of total RNA was passed though polyA column using the Oligotex kit (Qiagen). The 5'-RNA adapter containing a Mme I recognition site was ligated by T4 RNA ligase and further reverse transcribed to amplify the templates. After digesting with Mme I then ligated to a 3'-double DNA adapter, the products were amplified by additional PCR cycles and gel-purified for Illumina sequencing. The files contain the raw data of degradome sequencing.

2012-11-06 | GSE35739 | GEO

Excited-State Geometry Optimization of Small Molecules with Many-Body Green's Functions Theory.

Project description:We present a benchmark study of gas phase geometry optimizations in the excited states of carbon monoxide, acetone, acrolein, and methylenecyclopropene using many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation (BSE) employing numerical gradients. We scrutinize the influence of several typical approximations in the GW-BSE framework; we used one-shot G0W0 or eigenvalue self-consistent evGW, employing a fully analytic approach or plasmon-pole model for the frequency dependence of the electron self-energy, or performing the BSE step within the Tamm-Dancoff approximation. The obtained geometries are compared to reference results from multireference perturbation theory (CASPT2), variational Monte Carlo (VMC) method, second-order approximate coupled cluster (CC2) method, and time-dependent density-functional theory (TDDFT). We find overall a good agreement of the structural parameters optimized with the GW-BSE calculations with CASPT2, with an average relative error of around 1% for the G0W0 and 1.5% for the evGW variants based on a PBE0 ground state, respectively, while the other approximations have negligible influence. The relative errors are also smaller than those for CC2 and TDDFT with different functionals and only larger than VMC, indicating that the GW-BSE method does not only yield excitation energies but also geometries in good agreement with established higher-order wave function methods.

| S-EPMC7876808 | biostudies-literature

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules.

Project description:Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking have been parametrized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data. The energy function improves performance in a wide range of protein structure prediction challenges, including monomeric structure prediction, protein-protein and protein-ligand docking, protein sequence design, and prediction of the free energy changes by mutation, while reasonably recapitulating small-molecule thermodynamic properties.

| S-EPMC5515585 | biostudies-literature

Exon Level Machine Learning Analyses Elucidate Novel Candidate miRNA Targets in an Avian Model of Fetal Alcohol Spectrum Disorder

Project description:An RNA-seq dataset obtained from neural fold-stage chicken (Gallus gallus, strain Special Black) embryos that were exposed to a pharmacologically-relevant alcohol concentration (52 mM for 90 min) or isotonic saline. The cranial headfolds were isolated 6 hours following the initial alcohol exposure. Following RNA isolation, cDNA synthesis, and quality assurance (20), paired-end reads (75 bp) were generated on an Illumina Genome Analyzer IIx (University of Wisconsin Biotechnology Center).

2018-08-01 | GSE115383 | GEO

Synthesis, Optimization, and Evaluation of Novel Small Molecules as Antagonists of WDR5-MLL Interaction.

Project description:The WD40-repeat protein WDR5 plays a critical role in maintaining the integrity of MLL complexes and fully activating their methyltransferase function. MLL complexes, the trithorax-like family of SET1 methyltransferases, catalyze trimethylation of lysine 4 on histone 3, and they have been widely implicated in various cancers. Antagonism of WDR5 and MLL subunit interaction by small molecules has recently been presented as a practical way to inhibit activity of the MLL1 complex, and N-(2-(4-methylpiperazin-1-yl)-5-substituted-phenyl) benzamides were reported as potent and selective antagonists of such an interaction. Here, we describe the protein crystal structure guided optimization of prototypic compound 2 (K dis = 7 μM), leading to identification of more potent antagonist 47 (K dis = 0.3 μM).

| S-EPMC4027439 | biostudies-literature

Degradome analysis in Phalaenopsis aphrodite subsp. formosana

Project description:We performed one degradome sequencing for identification and characterization of novel microRNAs in Phalaenopsis aphrodite subsp. formosana. Plant tissues of leaves, stalk, and flower buds frozen in liquid nitrogen were ground to fine powder using a mortar and pestle, respectively. Total RNA extraction was freshly prepared using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. About 50 Î¼g of leaves with or without low temperature treatment, stalks and flower buds were taken separately and then mixed. The degradome library was constructed by the Genomics BioSci & Tech. Company following the manufactoring protocol. In brief, 200 Î¼g of total RNA was passed though polyA column using the Oligotex kit (Qiagen). The 5'-RNA adapter containing a Mme I recognition site was ligated by T4 RNA ligase and further reverse transcribed to amplify the templates. After digesting with Mme I then ligated to a 3'-double DNA adapter, the products were amplified by additional PCR cycles and gel-purified for Illumina sequencing. The files contain the raw data of degradome sequencing. Examination of one degradome of mixed tissues of Phalaenopsis orchid

2012-11-06 | E-GEOD-35739 | biostudies-arrayexpress

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