Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - 20200311_Pseudomonas_psychrophila_sp_JB418_MS2

ABSTRACT: P. psychrophila sp. JB418 was grown on 10% Cheese Curd Agar (CCA) for 3 days prior to extraction. For extraction, Acetonitrile was added to each culture and sonicated for 1hr, then solvent was removed and dried to afford a dry weighed extract. Extracts were then dissolved in either 100% (pooled replicates) or 90% (individual replicates) Methanol and LC-MS/MS was performed. Pooled replicate was run on a Bruker Impact II qTOF and individual biological replicates were run on a Bruker compact qTOF. Solvent B was ACN with 0.1% Formic Acid and Solvent A was water with 0.1% Formic Acid for both analyses, gradient of 10-100% B over the course of 10-12 minutes on a UPLC C18 column. File naming: JB418_alone = pooled biological replicate, JB418 followed by number = individual biological replicates, CCA = media controls and MeOH = solvent blanks.

INSTRUMENT(S): compact, impact

ORGANISM(S): Pseudomonas Psychrophila (ncbitaxon:122355)

SUBMITTER: Laura Sanchez

PROVIDER: MSV000085085 | GNPS | Wed Mar 11 11:42:00 GMT 2020

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Male BALB/c Mouse Testosterone-Treated Submandibular/Lacrimal/Meibomian Glands

Project description:Series includes pooled (n = 5 mice per biological replicate) samples from lacrimal, meibomian, and submandibular glands of male palcebo- and testosterone-treated BALB/c mice. All experiments were run in triplicate (pooled biological replicates) on CodeLink Mouse Uniset I Microarrays. Keywords: repeat sample

2004-11-24 | GSE1582 | GEO

Interaction between rhizobacterial community and host root metabolism influences poplar salt tolerance

Project description:<p>Poplar seedlings were cultivated in saline soil with low salt concentrations for 120 days, after which root tissues were harvested for untargeted metabolomic analysis. For each genotype, roots of three to four seedlings were pooled to form one biological replicate, with four biological replicates established per genotype.</p>

2026-05-15 | MTBLS14479 | MetaboLights

Transcriptome analysis of 6 hours post fertilization mecp2-null versus wild type zebrafish embryos

Project description:RNA sequencing was performed on RNA isolated from groups of 6 hpf wild type and mecp2-null embryos (n=3 biological replicates per condition with 30 embryos pooled per replicate). DESeq2 analysis was performed using https://usegalaxy.org/

2016-09-01 | GSE80348 | GEO

Comparison of endogenous and viral microRNA profile of Arabidopsis thaliana with and without Turnip Mosaic Virus infection.

Project description:Individual miRNA profile was identified for two Col-0 WT replicates and two Col-0 TuMV infected plant replicate samples, with 12-15 plants in each replicate.Comparison was done based on the microRNA expression profile in both biological replicates for infected and uninfected plant samples .

2010-06-27 | GSE22583 | GEO

Effect of 8-oxoguanine DNA glycosylase 1 (OGG1) inhibitor on pro-inflammatory gene expression.

Project description:Balbc J mouse received vehicle (solvent) or OGG1 inhibitor 1, 4, 8, 12, 24, 28 , 32, 36, 40 and 44h after RSV infection via intraperitoneal route. RSV (10^6 PFU) was installed into lungs via intranasal route in 60 microliters of solvent). One, 2, 3, 6, 12, 24, 48 and 72 hour after RSV challenge mice were sacrificed, lungs were removed and RNAs were isolated from individual lungs (n=6) After reverse transcription cDNAs were pooled and changes in gene expression was determined by using SABiosciences Mouse Inflammatory Cytokines & Receptors PCR Array (PAMM-011ZD)

2021-09-14 | GSE157630 | GEO

Single cell RNA sequencing analysis of the mouse colonic mesenchyme (Drop-seq)

Project description:Single cell RNA sequencing of the mouse colonic mesenchyme. Mesenchymal/lamina propria cells were isolated from the middle and distal colon of wild type mice in two biological replicates. For each biological replicate the colons of n = 2 mice were pooled. The vast majority of intestinal epithelial cells were depleted by Ethylenediaminetetraacetic acid (EDTA) treatment of the tissue samples and mesenchymal/lamina propria cells were isolated after enzymatic treatment with collagenase XI and dispase. Single cell RNA sequencing was performed with the Drop-seq protocol. N =5 Drop-seq collections (samples) were processed in total, two from the first biological replicate and three from the second.

2019-12-21 | GSE142423 | GEO

Small RNA genes of Physcomitrella patens

Project description:Small RNA-seq from 10 day-old wild-type Physcomitrella patens was performed using 5 biological replicates. Replicates were grown in three batches at different times. Batch 1 had one replicate from strain "old WT", Batch 2 had two replicates from strain "old WT", and batch 3 had two replicates from strain "2009 WT". Old WT and 2009 WT were collected from Gransden wood, England; "old" has been in lab cultivation for at least 10 years, while "2009" was more recently collected from the wild (in 2009.)

2015-06-30 | GSE44900 | GEO

ENCODE Transcript Mapping for Human Neutrophil (PMN) Total RNA

Project description:Transcript Mapping on Affymetrix ENCODE arrays for 10 different biological replicates of Neutrophil (PMN) Total RNA (each with 2 technical replicates). Each biological sample is from a different individual. Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays Keywords: other

2005-05-19 | GSE2678 | GEO

Nutlin-3a-induced changes in the proteome of parental and RFX7 knock-out U2OS cells

Project description:Mass spectrometry-based whole proteome analysis of parental and RFX7 knock-out U2OS cells treated with 10 µM Nutlin-3a or DMSO solvent control. Ten biological replicates were used.

2023-03-11 | PXD024869 | Pride

Inhibition of the hepatic vitamin B12-dependent methionine-salvage pathway by trichloroethylene metabolites accounts for the formic aciduria in the rat

Project description:The industrial solvent trichloroethylene (TCE) produces a marked formic aciduria in male and female F344 rats and in male C57Bl mice following single or multiple dosing. The two major metabolites of TCE formed by cytochromes P450 metabolism also produce formic aciduria. The quantity of formic acid excreted was about 2-fold higher following trichloroacetic acid (TCA) compared to trichloroethanol (TCE-OH) or TCE, at similar doses of 16mg/kg/day for 3 days. Prior treatment of male F344 rats with 1-aminobenzotriazole a cytochrome P450 inhibitor, followed by TCE, completely prevented the formic aciduria but had no effect on formic acid excretion produced by TCA, suggesting TCA is the proximate metabolite producing this response. Metabolism of formic acid is largely controlled by the vitamin B12 –dependent methionine salvage pathway. Transcriptomic analysis on the liver of rats dosed with 16mg/kg/day TCE for three days when compared to control liver showed nine differentially expressed genes, of particular interest was the down regulation of LMBRD1 involved in the conversion of vitamin B12 into one of two molecules, methylcobalamin (CH3Cbl) or S-adenosylcobalamin (AdoCbl). Administration of CH3Cbl or hydroxocobalamin for 3 days to rats given a single dose of TCE, lead to a reduction in formic acid in their urine. Similarly, rats given TCE followed by L-methionine for 3 days excreted less formic acid in their urine. These findings suggest an effect on the vitamin B12 –dependent methionine salvage pathway. This was supported by the finding that hepatic methionine synthase, which converts homocysteine to methionine, was inhibited following three large daily dose of TCE. We propose that TCE metabolites interact with the vitamin B12 -dependent methionine salvage pathway leading to tetrahydrofolate deficiency and increased excretion of formic acid in rat urine.

2020-11-20 | GSE122664 | GEO

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