Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabolic profiling with UPLC-MS orbitrap of diatoms Coscinodiscus granii infected with parasitic oomycete Lagenisma coscinodisci

ABSTRACT: The bloom-forming diatoms Coscinodiscus granii were cultivated in a non-contact dual cultivation apparatus. This device allows the exchange of exudates, without transfer of any microorganisms, allowing the investigation of both endo- and exo-metabolome. The treatment consisted in infecting diatom cells with parasitic oomycete Lagenisma coscinodiscii. At late infection stage (5 days of incubation), all cultures were recovered and filtrated and the endometabolome was investigated. The healthy cells which were exposed to the exudates of the infected cells were assigned as exposed cells. Healthy cell populations were taken as the controls. The experiment contained 6 replicates per conditions (control vs control, control/exposed vs treatment). Methanolic extractions of all cells were performed and metabolic profiles of the different conditions was conducted with UPLC-MS orbitrap.

INSTRUMENT(S): Liquid Chromatography MS - Positive (LC-MS (Positive))

PROVIDER: MTBLS775 | MetaboLights | 2019-09-23

REPOSITORIES: MetaboLights

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20171130_ma_f2.raw	Raw
	20171204_ma_3-10a.raw	Raw
	20171204_ma_3-10b.raw	Raw
	20171204_ma_3-11a.raw	Raw
	20171204_ma_3-11b.raw	Raw

Items per page:

1 - 5 of 60

Similar Datasets

Loqs-PD and R2D2 define independent pathways for RISC generation in Drosophila

Project description:In Drosophila, siRNAs are classified as endo- or exo-siRNAs based on their origin. Both are processed from double-stranded RNA precursors by Dcr-2, then loaded into the Argonaute protein Ago2. While exo-siRNAs serve to defend the cell against viruses, endo-siRNAs restrict the spread of selfish DNA in somatic cells, analogous to piRNAs in the germ line. Endo- and exo-siRNAs display a differential requirement for double-stranded RNA binding domain proteins (dsRBPs): R2D2 is needed to load exo-siRNAs into Ago2 while the PD isoform of Loquacious (Loqs-PD) stimulates Dcr-2 during the nucleolytic processing of hairpin-derived endo-siRNAs. In cell culture assays, R2D2 antagonizes Loqs-PD in endo-siRNA silencing and Loqs-PD is an inhibitor of RNA interference. Loqs-PD can interact via the C-terminus unique to this isoform with the DExH/D-helicase domain of Drosophila Dcr-2, where binding of R2D2 has also been localized. Separation of the two pathways is not complete; rather, the dicing and Ago2-loading steps appear uncoupled, analogous to the corresponding steps in miRNA biogenesis. Analysis of deep sequencing data further demonstrates that in r2d2 mutant flies, siRNAs can be loaded into Ago2 but not all siRNA classes are equally proficient for this. Thus, the canonical Ago2-RISC loading complex can be bypassed under certain circumstances. Examination of small RNAs from two different mutant strains as well as the corresponding heterozygous controls

2011-02-10 | E-GEOD-26230 | biostudies-arrayexpress

Loqs-PD and R2D2 define independent pathways for RISC generation in Drosophila

2011-02-10 | GSE26230 | GEO

Project description:EXO(C) VS EXO(S)

| PRJNA1004619 | ENA

Project description:M0+EXO(C) VS M0+EXO(S)

| PRJNA1004757 | ENA

Analysis to evaluate the presence of 5’ cap in intragenic lncRNAs

Project description:RNA aliquots were digested with 5’-phosphate-dependent exonuclease (5'-exo) following pre-treatment with tobacco acid pyrophosphatase (TAP) to release the 5’ cap and render the RNA susceptible to 5’ exonuclease digestion (TAP+/5'-exo+). Two color array hybridizations were performed and TAP+/5'-exo+ samples were compared with TAP-/5'-exo+ control samples. Two-condition experiment, TAP+/5'-exo+ vs. TAP-/5'-exo+ treated total RNA samples. Biological replicates: 4 with dye swap

2015-06-30 | E-GEOD-62984 | biostudies-arrayexpress

CROP: A Retromer- PROPPIN complex mediating membrane fission in the endo-lysosomal system

Project description:Endo-lysosomal compartments exchange proteins by fusing, fissioning, and through endosomal transport carriers. Thereby, they sort many plasma membrane receptors and transporters and control cellular signaling and metabolism. How the membrane fission events are catalyzed is poorly understood. Here, we identify the novel CROP complex as a factor acting at this step. CROP integrates PROPPIN Atg18 with a part of the endosome- and vacuole-associated retromer complex to generate a membrane fission device of much higher potency. We studied its activity in yeast, in human cells and on liposomes.

2022-05-05 | PXD031244 | Pride

Sindbis virus induces the production of a novel class of endogenous siRNAs in Aedes aegypti mosquitoes

Project description:We examined the biogenesis of mRNA-derived endogenous short-interfering RNAs (endo-siRNAs) in the disease vector mosquito, Aedes aegypti. Under standard conditions, mRNA-derived endo-siRNAs were produced from the bidirectional transcription of tail-tail overlapping gene pairs. Upon infection with the alphavirus, Sindbis virus (SINV), another class of mRNA-derived endo-siRNAs was observed. Genes producing SINV-induced endo-siRNAs were not enriched for overlapping partners or nearby genes, but were enriched for transcripts with long 3'UTRs. Endo-siRNAs from this class derived uniformly from the entire length of the target transcript, and were found to regulate the transcript levels of the genes from which they were derived. Strand-specific qPCR experiments demonstrated that antisense strands of targeted mRNA genes were produced to exonic, but not intronic regions. Finally, small RNAs mapped to both sense and antisense strands of exon-exon junctions, suggesting double-stranded RNA precursors to SINV-induced endo-siRNAs may be synthesized from mature mRNA templates. These results suggest additional complexity in small RNA pathways and gene regulation in the presence of an infecting virus in disease vector mosquitoes. Examination of endo-siRNA production in Aedes aegypti mosquitoes

2012-04-01 | E-GEOD-35161 | biostudies-arrayexpress

The hub protein Loqs connects the miRNA and endo-siRNA pathways in mosquitos

Project description:Aedes aegypti mosquitoes vector several arboviruses of global health significance, including dengue viruses and chikungunya virus. RNA interference (RNAi) plays an important role in antiviral immunity, gene regulation and protection from transposable elements. Double-stranded RNA binding proteins (dsRBPs) are important for efficient RNAi; in Drosophila functional specialization of the miRNA, endo-siRNA and exo-siRNA pathway is aided by the dsRBPs Loqs-PB, Loqs-PD and R2D2, respectively. However, this functional specialization has not been investigated in other dipterans. Characterization of the gene structure, expression pattern and interactions with other RNAi/miRNA components revealed that mosquito Loqs/R3D1 isoform -PA, but not -PB interacted readily with both AeAGO1 and AeAGO2. This interaction was mapped to a 32 a.a. region predicted to be structurally similar to the unique 22 a.a. tail of Drosophila Loqs-PD. No -PD isoforms could be detected in Ae. aegypti; analysis of other dipteran genomes demonstrated that this isoform is not conserved outside of Drosophila. Overexpression experiments indicated that Loqs/R3D1-PA participates in endo-siRNA, but not exo-siRNA based silencing. We conclude that the functional specialization of Loqs-PD in Drosophila is a recently derived trait, and that in other dipterans, including the medically important mosquitoes, Loqs/R3D1-A participates in both the miRNA and endo-siRNA based pathways. 12 samples, 3 replicates of each type of sample. The GFP sample is the reference sample

2015-04-08 | E-GEOD-65070 | biostudies-arrayexpress

Murine lung: Control vs Diesel Exhaust Exposed

Project description:Murine lung: Control vs Diesel Exhaust Exposed

| PRJNA941937 | ENA

Phaeodactylum tricornutum

Project description:Phaeo CDF 2011 - stressor exposed vs control

| PRJNA151089 | ENA