Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Celastraceae_plant_extracts_library

ABSTRACT: This is an untargeted liquid chromatography high resolution mass spectrometry profiling data set of 76 samples of different plant parts of 36 species belonging to 14 genera of the Celastraceae family. The data set is composed of: the .raw and open format .mzML files; the metadata associated to each file, including the curated accepted taxonomy based on the Open Tree of Life, analytical and biological tissue characteristics.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Several Species

SUBMITTER: Jean-Luc Wolfender

PROVIDER: MSV000087970 | MassIVE | Wed Aug 11 07:15:00 BST 2021

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Publications

<i>Inventa</i>: A computational tool to discover structural novelty in natural extracts libraries.

Quiros-Guerrero Luis-Manuel LM Nothias Louis-Félix LF Gaudry Arnaud A Marcourt Laurence L Allard Pierre-Marie PM Rutz Adriano A David Bruno B Queiroz Emerson Ferreira EF Wolfender Jean-Luc JL

Frontiers in molecular biosciences 20221111

Collections of natural extracts hold potential for the discovery of novel natural products with original modes of action. The prioritization of extracts from collections remains challenging due to the lack of a workflow that combines multiple-source information to facilitate the data interpretation. Results from different analytical techniques and literature reports need to be organized, processed, and interpreted to enable optimal decision-making for extracts prioritization. Here, we introduce ...[more]

PMID: 36438653

Similar Datasets

GNPS - Celastraceae_plant_extracts_library

Project description:This is an untargeted liquid chromatography high resolution mass spectrometry profiling data set of 76 samples of different plant parts of 36 species belonging to 14 genera of the Celastraceae family. The data set is composed of: the .raw and open format .mzML files; the metadata associated to each file, including the curated accepted taxonomy based on the Open Tree of Life, analytical and biological tissue characteristics.

2021-08-11 | MSV000087970 | GNPS

Dermatophytes CGH based on a Trichophyton rubrum cDNA microarray

Project description:A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and comparative genome hybridization based on microarray procedures were carried out. Dermatophyte species are classified into three genera: Epidermophyton, Microsporum, and Trichophyton. To determine the relationship between these three groups comparative genome hybridization were used in our experiment. Trichophyton rubrum genmic DNA was reference DNA and labelled by Cy3 while the other dermatophytes genomic DNA were test DNA and labelled by CY5. Test and reference DNA were co-hybridized with the T. rubrum cDNA microarray and the numbers of genes shared between each species and T. rubrum were determined. Keywords: Comparative Genomic Hybridization We used a Trichophyton rubrum cDNA microarray prepared in our lab through comparative genome hybridization of genomic DNA of 21 dermatophyte strains (belonging to 20 species) to elucidate the taxonomy and evolution profiles of 20 dermatophyte species. The numbers of genes shared between each species and T. rubrum were determined. Each strain DNA hybridized for 3 times. The slides were separated into three groups base on different datasets.

2010-05-03 | E-GEOD-7909 | biostudies-arrayexpress

RNA-Seq of WT and -P treatment

Project description:To further explore the molecular mechanisms of P regulation in banana plants, we used RNA sequencing-based transcriptomic analysis for banana plants subjected to Pi deficit stress for 60 days.We detected 1900 significantly differentially expressed genes (DEGs) in aboveground plant parts and 7398 DEGs in root parts under low P stress. Gene ontology (GO) classification analysis showed that 156,291 GO terms belonging to molecular functions, 53,114 GO terms belonging to cellular components, and 228,544 GO terms belonging to biological processes were enriched in the aboveground and root components. A number of DEGs involved in energy metabolism-related processes, signal transduction, control of rhizosphere P activation, and Pi mobilization were found, which were confirmed by quantitative reverse-transcription PCR (RT-PCR) analysis. At the transcriptomic level, we detected 13 DEGs from different organs and with different functions in the time-course response to phosphorus deficiency stress. These DEGs may include some key genes that regulate the phosphorus network, increasing our understanding of the molecular mechanism of Pi homeostasis in banana.

2018-06-15 | GSE115792 | GEO

High-throughput Illumina Hiseq2000 seuqencing of small RNAs from Hevea brasiliensis PB260 and PB217 clones

Project description:MicroRNAs (miRNAs) are non-coding, short, single-stranded RNAs with essential roles in gene regulation in various organisms including higher plants. In contrast to the vast information on miRNAs from many economically important plants, almost nothing has been reported on the identification or analysis of miRNAs from rubber tree (Hevea brasiliensis L.), the most important natural rubber-producing crop. To identify miRNAs and their target genes in rubber tree, high throughput sequencing combined with a computational approach was performed. Four small RNA libraries were constructed for deep sequencing from mature and young leaves of two rubber tree clones, PB 260 and PB 217, which provide high and low latex yield, respectively. 237 miRNAs belonging to 37 known miRNA families were identified, and northern hybridization validated miRNA expression and revealed developmental stage-dependent and clone-specific expression for some miRNAs. We took advantage of the newly released rubber tree genome assembly as well as the genomic databases from leafy spurge and cassava, two species related to rubber tree, and predicted 15 novel miRNAs. 4 samples examined: PB260 mature leaves, PB260 young leaves, PB217 mature leaves, and PB217 young leaves.

2012-04-02 | E-GEOD-35254 | biostudies-arrayexpress

Sloth collagen phylogenetics - The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies (Antilles)

Project description:The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies (Antilles). To date, molecular evidence has played only a minor role in folivoran systematics, as most recently-extinct species lived in places not conducive to DNA preservation. Here we utilize collagen sequence information to assess the relationships of tree sloths to a large sample (13 species) of extinct Quaternary folivorans.

2019-06-07 | PXD012859 | Pride

High-throughput Illumina Hiseq2000 seuqencing of small RNAs from Hevea brasiliensis PB260 and PB217 clones

2012-04-03 | GSE35254 | GEO

RNA-Seq Based Reconstruction of the Phylogenetic Tree of the Genus Flaveria (Asteraceae)

Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.

2015-01-08 | E-GEOD-54339 | biostudies-arrayexpress

Nassar2022 - Metagenomics Classification Task for Scientific Literature Text

Project description:This is a use case to show that, given any automatic metagenomic classification model for the documents, we can convert those to ONNX (Open Neural Network Exchange) format; it also consists of the Dockerfile that can be used to prepare a docker image. This conversion ensures interoperability and open access. The ONNX format utility can perform the following essential tasks: model conversion, inference, inspection, and optimization. Reference: 1) https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/9 2) https://www.ebi.ac.uk/biomodels/search?query=Maaly+Nassar&domain=biomodels 3) https://gitlab.com/maaly7/emerald_metagenomics_annotations 4) This model is built upon the model of the following publication: Maaly Nassar, Alexander B Rogers, Francesco Talo', Santiago Sanchez, Zunaira Shafique, Robert D Finn, Johanna McEntyre, A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications, GigaScience, Volume 11, 2022, giac077, https://doi.org/10.1093/gigascience/giac077

2023-05-25 | BIOMD0000001068 | BioModels

Silver resistance in Gram-negative bacteria

Project description:High Frequency of Silver Resistance in Invasive Isolates Belonging to Genera Enterobacter and Klebsiella

| PRJEB9556 | ENA

Transcriptome dynamics during adventitious root formation in cuttings of Cryptomeria japonica D.Don

Project description:To reveal transcriptome dynamics during adventitious root formation in a coniferous tree, C. japonica, we conducted custom microarry experiments. Three parts from cuttings of easy-to-root clone of C. japonica were collected at eight time points during adventitious root formation. The results revealed major turning points on transcriptome toward adventitious root formation and the expression behavior of genes related to carbohydrate, plant hormone and others suggested the important biological changes for adventitious root formation.

2018-12-25 | GSE102874 | 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