GNPS - salvia officinalis samples format mzML LCMS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LCMS-8045
ORGANISM(S): Salvia Officinalis (ncbitaxon:38868)
SUBMITTER: 
Natalia Pachura
PROVIDER: MSV000090117 | GNPS | Fri Aug 12 03:31:00 BST 2022
REPOSITORIES: GNPS
Similar Datasets
Project description:Salvia officinalis- extracts obtain from herb subjected to convective drying at 40 degrees. Exctract obtained by maceration in eighty percent of methanol.
2022-08-12 | MSV000090117 | MassIVE
Project description:This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers. Keywords: Reference design
2008-02-13 | GSE10483 | GEO
Project description:We carried out a prospective, longitudinal, single-center, observational cohort study of patients with confirmed acute methanol poisoning that were treated in hospitals during a mass methanol poisoning outbreak in the Czech Republic in 2012. Venous blood for proteomic analysis was obtained from 24 patients with confirmed acute methanol poisoning upon admission to the hospital (group M (“Methanol”)) with heparin administration for hemodialysis and ethanol or fomepizole administration as the antidote to block ADH. In the follow-up group of survivors of methanol poisoning (group S (“Survivors”)), venous blood samples for proteomic analysis were obtained from 46 patients during the examination, which took place 4 years after discharge from the hospital. For the control group not exposed to methanol, 24 healthy subjects were recruited (group C, “Controls”). Blood samples were spun, the serum was separated, and the samples were frozen to −80 °C until the analyses. Blood serum samples were depleted of most abundant serum proteins using Agilent MARS 14 column, samples fractionated and fractions containing proteins of interest precipitated. Samples were analyzed using LC-MS/MS Thermo Orbitrap Fusion (UHPLC-ESI-Q-OT-qIT) and identified proteins with differential expression.
2022-12-12 | PXD035726 | Pride
Project description:Introduction: The application of single-cell RNA sequencing has greatly improved our under-standing of various cellular and molecular mechanisms involved in physiological and pathophysi-ological processes. However, obtaining living cells for this technique can be difficult under certain conditions. To solve this problem, the methanol fixation method appeared as a promising alternative for routine clinical use. Materials and Methods: In this study, we selected two AML samples that had been fixed in methanol for 12–18 months. Once the cells were rehydrated, these samples were subjected to single-cell RNA sequencing. We then compared the results obtained from these samples with those obtained from the same samples cryopreserved in DMSO. Results: We used a previously validated methanol fixation protocol to perform scRNA-seq on DMSO cryopreserved cells and cells fixed in methanol for more than one year. Preliminary results show that methanol fixation induces some genetic and transcriptional modification compared with DMSO cryopreservation but remains a valuable method for single-cell analysis of primary human leukemia cells. Conclusions: The initial findings from this study highlight certain resemblances in methanol fixation over a 12-month period and cryopreservation with DMSO, along with associated transcriptional level modifications. However, we observed genetic degradation in the fixation condition when extending beyond one year. Despite certain study limitations, it is evident that short-term methanol fixation can be effec-tively used for leukemia blast samples. Its ease of implementation holds the potential to simplify the integration of this technique into routine clinical practice.
2023-08-17 | GSE237239 | GEO
Project description:Single-cell sequencing technologies are revolutionizing biology, but are limited by the need of dissociating fresh samples that can only be fixed at later stages. We present ACME (ACetic-MEthanol) dissociation, a species-versatile cell dissociation approach that fixes cells as they are being dissociated. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, can be sorted by Fluorescence-Activated Cell Sorting (FACS) and are permeable, enabling combinatorial approaches of single-cell transcriptomics. ACME is based on cheap reagents and it can be done in most labs and even sampling trips. As a proof of principle, we have performed SPLiT-seq with ACME cells to obtain around ~35K cells from two planarian species and identified all previously described cell types in similar proportions. This technique allows fixed, dissociated cells to be obtained from diverse organisms that can be cryopreserved and subjected to combinatorial barcoding methods for single-cell transcriptomics and thus will accelerate our knowledge of cell types across the tree of life.
2020-06-03 | GSE150259 | GEO
Project description:The goal was to obtain expression data from the deep cones in early human hypertrophic scars to be used to confirm expression data obtained in a porcine model.
2011-12-31 | GSE26213 | GEO
Project description:To obtain a global view of the response of S. flexneri at the expression level induced by temperature up-shift, we compared the expression profiles of log-phase and stationary-phase cells grown at 30 degrees and 37 degrees Celsius.
2010-06-02 | GSE16535 | GEO
Project description:In this data set we investigate dynamic differences in the transcriptome between 37 and 40 degrees C after treatment with TNFalpha. In the continuous temperature experiments, cells were grown at 37 degrees C and were then left at 37 degrees C, or transferred to 40 degrees C, for 1hour after which they (at time 0) were stimulated with 10 ng/ml of TNFα . Measurements were taken at 0, 30, 130, 230 and 430 minutes. In the 'switch' experiment, cells were grown the same way but the temperature of the incubator was turned up to 40 degrees C after 200 minutes. Measurements were taken at 230 and 430 minutes.
2018-04-05 | E-MTAB-5158 | biostudies-arrayexpress
Project description:Analysis of microRNA expression at 37 and 40 degrees shows a novel class of microRNAs that regulate fever. Arrays of gene expression at 37 and 40 of THP-1 derived macrophages as well as a thermomiR knockdown experiment.
2015-05-29 | GSE69343 | GEO
Project description:Samples for metabolomic analysis were prepared as follows. A 200 uL aliquot of bacterial cultures or control medium (prepared, as described in the above section) was mixed with 800 uL of 99.5 percent ethanol (Fisher Scientific) and subjected to 3 rounds of freeze thaw cycles: 10 minutes at -80C, 8 minutes at room temperature. Next, samples were spun down for 10 minutes at 16,000g, 4C to remove cell debris, and supernatants were transferred to new tubes. Ethanol supernatants were stored at -80C until further extraction. Each ethanol extraction was performed in two technical duplicates.
The solid phase extraction (SPE) of the ethanol extracts was performed with the Oasis HLB 96-well plate (30 mg Sorbent per Well, 30 um Particle Size) (Waters Corporation) set up with a vacuum pump manifold. Each well of the plate was washed with 700 uL of 100 percent HPLC-grade methanol and equilibrated with 700 uL of HPLC-grade water. Next, 400 uL of ethanol extracts were added to the wells and allowed to slowly elute. Wells were next washed with 800 uL of 5 percent methanol in water. Metabolites from bacterial cultures or control media were eluted with 200 uL of 100 percent methanol. Vacuum up to 20 psi was applied for the wells that did not elute within one hour. The collected eluted metabolites were stored at -20 until the HPLC-MS analysis. The HPLC-MS analysis of extracted metabolites was performed with the use of a Dionex UltiMate 3000 UHPLC system (Fisher Scientific) coupled to a Bruker impact HD quadrupole time-of-flight mass spectrometer (Bruker). The chromatographic separation was performed on a Kinetex C18 1.7 um, 100A UHPLC column (50 mm x 2.1 mm) (Phenomenex), held at 40C during analysis. 5 uL of each sample was injected. Mobile phase A was water, 0.1 percent v:v formic acid, and mobile phase B was acetonitrile, 0.1 percent v:v formic acid. The solvent gradient table was set as follows: 2 percent B, increased to 10 percent B over 0.2 min, then to 100 percent B at 12 min, held at 100 percent B for 1.5 min, decreased back to 2 percent B in 0.5 min, followed by washout cycle and equilibration; total analysis time of 15 min. The scanned m/z range was 80-2000 Th; capillary voltage 4,500 V; nebulizer gas pressure 2 bar, drying gas flow rate 9 l min-1 and temperature 200C. The full MS scan was followed by a tandem mass spectrometry fragmentation of the seven most abundant ions within the spectrum. For tandem mass spectrometry, the collision cell collision energy was set at 3 eV and the collision energy was stepped 50 percent, 75 percent, 150 percent, and 200 percent. The scan rate was 3 Hz. A HP-921 lock mass compound was infused during the analysis for post processing mass correction.
2022-10-17 | MSV000090542 | MassIVE