Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Rosmarinus officinalis - Rosemary plant - 3D molecular cartography

ABSTRACT: Dataset of 3D molecular cartography of Rosmarinus officinalis

INSTRUMENT(S): Maxis II qTOF

ORGANISM(S): Salvia Rosmarinus (ncbitaxon:39367)

SUBMITTER: Pieter Dorrestein

PROVIDER: MSV000080553 | GNPS | Thu Feb 16 22:13:00 GMT 2017

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A 3D molecular atlas of the chick embryonic heart

Project description:We performed a detailed analysis of gene expression in the 2-day (HH12) embryonic chick heart. RNA-seq of 13 microdissected heart regions reveals regionalised expression of about 15,000 genes (Dataset 1). Of these, 131 genes that are differentially expressed (FPKM ≥20, fold change ≥1.1-4.0) within a region compared to the other 12 regions were studied by in situ hybridisation (bold text in Dataset 1) and used to generate a 3D molecular map of the heart at this stage of development.

2019-10-02 | E-MTAB-7663 | biostudies-arrayexpress

3D genome topology distinguishes molecular subgroups of medulloblastoma

Project description:3D genome topology distinguishes molecular subgroups of medulloblastoma

| PRJNA1031604 | ENA

3D genome topology distinguishes molecular subgroups of medulloblastoma

Project description:Four main medulloblastoma (MB) molecular subtypes have been identified based on transcriptional, DNA methylation and genetic profiles. However, it is currently not known whether MB subtypes have their own specific 3D genome architecture. Hi-C maps were globally stable across MB subtypes. However, among the 3D genome features we tested, boundary strengths of topologically associating domains (TADs) were the best at classifying MB samples – including Group 3 and Group 4 specimens - according to their known molecular subtypes. Although boundary strength was not generally associated with differential gene expression between subtypes, we found that Group 3 and Group 4 specimens had differential TAD boundary strengths near genes that are uniquely expressed in their respective lineages of origin. Accordingly, we provide examples of TAD boundary reorganization that clearly distinguish Group 3 and 4 samples at these developmentally important genomic sites. TAD boundary strength allows classification of MB molecular subtypes, indicating that the shape of the 3D genome is unique to each molecular subtype. Genome topologies of Group 3 and 4 tumors are shaped differently at key lineage genes, but these differences are not strongly predictive of changes in gene expression. 3D genome architecture might be a fossil of the lineages of origin of MB subtypes.

2024-09-29 | GSE246125 | GEO

A 3D molecular atlas of the chick embryonic heart

Project description:A 3D molecular atlas of the chick embryonic heart

| PRJEB31198 | ENA

Microenvironment remodeling during human iPSC-derived NSC 3D differentiation

Project description:Brain microenvironment plays an important role in neurodevelopment and function, where extracellular matrix (ECM) components and soluble factors modulate cellular features, as migration, proliferation survival and neuronal function. Disruption of microenvironment’s homeostasis is often related to pathological conditions. Here, we addressed the microenvironment remodeling occurring during in vitro differentiation of human neural stem cells (NSC) in a three-dimensional (3D) culture system. Proteome and transcriptome dynamics revealed significant changes namely at cell membrane and ECM composition during 3D differentiation, diverging significantly from the profile of monolayer cultures (2D). Structural proteoglycans typically found in brain ECM were enriched during 3D differentiation, while 2D cultures presented increased levels of basement membrane constituents (e.g., laminins, collagens and fibrillins). Moreover, higher expression levels of synaptic machinery and ion transport machinery constituents observed for 3D cultures, both at mRNA and protein levels, suggested a higher degree of neuronal maturation and organization relative to 2D differentiation. This work demonstrated that neural cellular and extracellular features can be recapitulated in the presented 3D neural cell model, highlighting its value to address molecular defects in cell-ECM interactions associated with neurological disorders. <html><head>Associated GEO dataset is available at</head><body><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi">GSE102139</a></body></html>

2018-07-31 | PXD007130 | Pride

3D Laparoscopy Versus 2D Laparoscopy

Project description:* To compare surgical and oncological outcomes in patients underwent to colorectal resection with 3D vs 2D laparoscopic technique. * To evaluate the visual overload in surgeons using 3D laparoscopic technique.

| 2220465 | ecrin-mdr-crc

3D molecular cartography of the Panamanian rocket frog Colostethus panamansis (Dendrobatidae)

Project description:Data collected from specimens of C. panamansis for creating a 3D mapping.

2019-02-26 | MSV000083487 | MassIVE

Feature-based molecular networking in the GNPS analysis environment.

Project description:Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.

| S-EPMC7885687 | biostudies-literature

Expression data from Neural Progenitor cells cultured on 2D flat surfaces and in 3D scaffolds

Project description:A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheres (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level Neural progenitor cells were cultured on 2D surfaces, in 3D scaffolds and as 3D neural spheres. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared.

2009-12-22 | E-GEOD-13715 | biostudies-arrayexpress

Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas

Project description:Transcriptional profiling of 3D-retinas differentiated from mouse iPS cells comparing vehicle control- with 4-OHT-treated. 4-OHT is an inverse agonist of estrogen-related receptor beta (ERRÎ²), a rod-enriched transcription factor responsible for maintenance of rod photoreceptor cells and the treatment induces photoreceptor specific cell death in the 3D-retinas. Goal was to understand the mechanism of 4-OHT-induced degeneration of photoreceptor cells in the 3D-retinas. 4-OHT-induced gene expression in the 3D-retinas was measured at DD 26 when the photoreceptor cells were degenerated. Two-condition experiment, vehicle control- vs. 5 ÂµM 4-OHT-treated 3D-retinas. Biological replicates: each sample has 24 3D-retinas and 1 replicate.

2016-07-05 | E-GEOD-83985 | 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