Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Bacterial extracts from Spur Estremadura

ABSTRACT: Crude extracts produced by marine bacteria recovered from Spur Stremadura, Portugal.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Verrucosispora (ncbitaxon:84593) Saccharomonospora (ncbitaxon:1851) Stackebrandtia (ncbitaxon:283810) Nocardiopsis (ncbitaxon:2013) Actinomadura (ncbitaxon:1988) Streptomyces (ncbitaxon:1883) Micromonospora (ncbitaxon:1873) Saccharopolyspora (ncbitaxon:1835)

SUBMITTER: Susana Gaudencio

PROVIDER: MSV000085864 | GNPS | Fri Jul 31 17:19:00 BST 2020

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - Bacterial extracts from Brazilian Rocas Atoll - update

Project description:LC-MS/MS data of crude extracts produced by isolated bacteria recovered from Brazilian Rocas Atoll. The bacteria whose extracts were cytotoxic on tumor cell lines were identified by 16S rRNA.

2019-03-20 | MSV000083601 | GNPS

Dataset Workshop on Advanced Mass Spectometry 2025

Project description:LC-MS/MS data of crude extracts produced by isolated bacteria recovered from Brazilian Rocas Atoll. Subset of MSV000083601 for use as an example dataset on the Workshop on Advanced Mass Spectometry 2025.

2025-12-09 | MSV000100158 | MassIVE

Small RNA-seq from FPLC-fractionated leaf and flower crude extracts

Project description:Small RNA-seq from FPLC-fractionated leaf and flower crude extracts

| PRJNA540255 | ENA

GNPS - Salinispora species from Brazil

Project description:LC-Ms/MS data (ion-trap) of crude extracts produced by Salinispora species recovered from Brazil

2020-06-15 | MSV000085589 | GNPS

Transcriptional control in Candidatus Pelagibacter ubique and other marine bacterial taxa

Project description:Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere.

2015-03-03 | GSE66443 | GEO

Small RNA-seq from FPLC-fractionated leaf and flower crude extracts

Project description:Background: RNA interference (RNAi) is an indispensable regulatory mechanism governing developmental processes and stress responses via sequence-specific control of target RNAs mediated by the action of small, 20–24-nt-long, non-coding regulatory (s)RNAs such as micro (mi) and small interfering (si) RNAs. Biogenesis and sorting of miRNAs into ARGONAUTE (AGO) proteins are intensively investigated, however very few information is available about the presence and distribution of distinct sRNA pools in plant cells. Results: High-throughput sequencing of size-separated sRNA pools of plant crude extracts revealed that the majority of the canonical miRNAs were associated with high molecular weight RNA-induced silencing complexes co-migrating with AGO1 (HMW RISC). In contrast, the majority of 24-nt-long siRNAs were found in association with low molecular weight complexes co-migrating with AGO4 (LMW RISC). Intriguingly, we identified a large set of sRNAs in the cytoplasm, including mature miRNA sequences, in the low molecular size range corresponding to protein-unbound sRNAs. By comparing the RISC-loaded and protein-unbound pools of miRNAs, we identified miRNAs with highly different loading efficiencies. Investigation of some selected miRNAs in a transient expression system validated this finding. We also showed that the availability of RISCs is a limiting factor determining the loading efficiency of miRNAs. Conclusion: Our data reveal the existence of a regulatory checkpoint, likely controlled by information carried by the diverse miRNA precursors, determining the RISC-loading efficiencies of various miRNAs by sorting only a subset of the produced miRNAs into the biologically active RISCs.

2019-07-29 | GSE130431 | GEO

Transcriptional control in Candidatus Pelagibacter ubique and other marine bacterial taxa

2015-03-03 | E-GEOD-66443 | biostudies-arrayexpress

Functional Genomics Screen with Pooled shRNA Library and Gene Expression Profiling with Extracts of Azadirachta indica Identify Potential Pathways for Therapeutic Targets in Head and Neck Squamous Cell Carcinoma

Project description:We investigate the molecular targets and pathways that the neem extracts and the associated compounds act through, to bring about tumor suppression by using a genome-wide functional pooled shRNA screen on head and neck squamous cell carcinoma cell line treated with crude neem leaf extracts. We analyzed differences in global clonal sizes of the shRNA-infected cells cultured under no treatment and treatment with neem leaf extract conditions, assayed using next-generation sequencing. We further analyzed differences in gene expression in HSC-4 cells, upon treatment with neem leaf extract in a time-dependent manner, followed by a time-dependent rescue. Our results indicate that neem extract simultaneously affects various important molecular signaling pathways in head and neck cancer cells, some (TGF-β/HSF-1) of which may be therapeutic targets for this devastating tumor.

2019-01-15 | GSE125021 | GEO

Vibrio parahaemolyticus gene expression affected by 0.04% bile

Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. Strain RIMD 2210633, the wild type strain of the organism, causes acute gastroenteritis in humans. Human intestinal factor bile often affects the global gene regulation in some species of enteropathogenic bacteria. To determine the genes in V. parahaemolyticus that respond to bile, we investigated the differences in the transcriptomes of the wild type strain and the vtrA-null strain grown in Luria-Bertani medium cultivated with or without 0.04% crude bile. The vtrA gene encodes the previously identified T3SS2 regulator. Our goal is to demonstrate bile regulon controlled by VtrA in V. parahaemolyticus.

2010-10-10 | GSE21666 | GEO

Effectiveness of co-cultured Myristica fragrans Houtt. seed extracts with commensal Staphylococcus epidermidis and its metabolites in anti-microbial activity and biofilm formation of skin pathogenic bacteria

Project description:Skin commensal bacteria (Staphylococcus epidermidis) can help defend against skin infections, and they are increasingly being recognized for their role in benefiting skin health. This study aims to demonstrate the activities that Myristica fragrans Houtt. seed extracts, crude extract (CE) and essential oil (EO), have in terms of promoting the growth of the skin commensal bacterium S. epidermidis and providing metabolites under culture conditions to disrupt the biofilm formation of the common pathogen Staphylococcus aureus.

2025-09-01 | PXD055409 | JPOST Repository

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