GNPS - Chemical Standard to GNPS Library - GNPS00002 DO NOT USE
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Not Applicable
SUBMITTER: 
Alan Jarmusch Pieter Dorrestein
PROVIDER: MSV000084287 | GNPS |
REPOSITORIES: GNPS
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Project description:This is the second dataset for the new Chemical Standard to GNPS Library SOP workflow MSMS-Chooser Uploaded and run by the Dorrestein Lab.
These are the re-run samples from plate 2, after the instrument was fixed.
2019-10-23 | MSV000084494 | GNPS
Project description:The identification of putative biomarkers for predicting abdominal aortic aneurysm (AAA) progression can be achieved through proteomic strategies, particularly with shotgun proteomics. However, the heterogeneity of AAA tissue poses challenges for tissue homogenization and protein extraction, compromising reproducibility, an essential factor for clinical translation. Thus, we aimed to optimize a protocol for AAA tissue homogenization and protein extraction and to develop a standard operating procedure (SOP) to maximize protein yield and foster reproducibility in the field. In this context, several experimental variables were systematically tested in a bead-beating method for tissue homogenisation, including bead size (1.4 mm versus 2.8 mm of diameter), the number of extraction cycles (one up to three), a bead-to-tissue mass ratio at 20, 30, or 40, the lysis buffer-to-tissue ratio (10, 15, or 20 μL/mg), and the lysis buffer composition (RIPA, Urea/thiourea, and HEPES). Optimal conditions for protein extraction were achieved using 1.4 mm zirconium dioxide beads in two homogenization cycles, with a bead-to-tissue mass ratio of 30:1 and a lysis buffer-to-tissue ratio of 20 μL lysis buffer per milligram of tissue, in 2 mL O-ring cryotubes. Depending on the purpose of downstream analysis, recommendations for the use of each lysis buffers were provided based on their specific performance across specific indexes. In this context, HEPES and Urea/Thiourea buffers are recommended for studies prioritizing quantification reproducibility, while RIPA buffer is advised for protein extraction reproducibility. As a proof of concept, the optimized SOP was applied to characterize the AAA tissue proteome and several processes and pathways relevant in AAA pathophysiology were highlighted, including blood coagulation, cellular responses to stress, neutrophil degranulation, wound healing, and pathways of the immune system. Additionally, the enrichment analysis identified ECM remodeling and platelet activation, and degranulation as strongly represented pathways across the functional analysis for each buffer, reinforcing their contribution to aneurysm pathophysiology. Hence, these findings demonstrated that the SOP is well-suited for identifying disease-relevant biomarkers and therapeutic targets.
2026-01-05 | PXD060417 | Pride
Project description:This SuperSeries is composed of the SubSeries listed below. Data for miR-429, miR-205, miR-200b, and miR-141 were each compared independently to the same negative control data contained in the raw .CEL files nc-miR-1-1.CEL, nc-miR-1-2.CEL and nc-miR-1-3.CEL. For each miRNA, the negative control data were re-normalized together with data only from that specific miRNA. The experiment for M12 was performed at a later date and an independent set of negative control data was collected at that time. Therefore, only M12 data was compared to the negative control data contained in the raw .CEL files nc-miR-2-1.CEL, nc-miR-2-2.CEL, and nc-miR-2-3.CEL.
2015-01-30 | E-GEOD-56973 | biostudies-arrayexpress
Project description:Transcription factors have been implicated in the specification and differentiation of all cells in the mammalian retina with several transcription factors controlling the development of multiple neuronal subclasses. Horizontal cells and cone photoreceptors share a particularly intimate functional relationship but have been previously thought to develop through separate and distinct intrinsic molecular processes. We demonstrate that the zinc finger transcription factor Sall3 regulates development of both S-cone photoreceptors and horizontal cells. Our data shows that loss of function of Sall3 down-regulates the horizontal cell specific transcription factor Lhx1 and subsequently causes ectopic formation of horizontal-like wide-field amacrine cells partially phenocopying Lhx1-/- mice. Additionally, horizontal cells which laminate appropriately in Sall3 knockout mice show abnormal horizontal cell gene expression and failures in dendritic arborization. Over-expression of Sall3 also partially re-specifies cells to a horizontal-like wide-field amacrine fate. Intriguingly, Sall3 loss of function experiments also generated a massive reduction in the number of S-cone photoreceptors with remaining S-cones showing deficiencies in S-cone gene expression and morphology. Conversely, over-expression of Sall3 resulted in the ectopic expression of the S-cone specific genes S-opsin (Sop) and cone arrestin (Arr3) in electroporated cells. Our studies reveal that Sall3 regulates aspects of horizontal cell development in two ways: first, by maintaining Lhx1 expression, and second, by directly regulating expression of horizontal cell specific genes. We also show that Sall3 is an essential regulator of S-cone development in the mammalian retina and a potent activator of Sop and Arr3.
2011-09-10 | GSE24083 | GEO
Project description:To identify CNS endothelial cell (EC) the gene cohorts that participate in blood brain barrier (BBB) formation versus maintenance. We investigated the mechanism behind the reduced Wnt/β-catenin signaling observed in during later development We also investigated whether the adult endothelial cells can re express the EC gene cohorts required for the BBB formation.
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Project description:Alcohol use disorder (AUD) affects transcriptomic, epigenetic and proteomic expression in several organs including the brain. Multi-omic analyses of the brain from individuals with AUD to date lack a comprehensive analysis of protein alterations in the multiple brain regions that underlie neuroadaptations occurring in AUD. We performed quantitative proteomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of human post-mortem tissue from brain regions that play a key role in the development and maintenance of AUD: amygdala (AMG), hippocampus (HIPP), hypothalamus (HYP), nucleus accumbens (NAc), prefrontal cortex (PFC) and ventral tegmental area (VTA). Brain tissues analyzed were from individuals with AUD (n = 11) and matched controls (n = 16).
2023-10-24 | PXD040884 | Pride
Project description:RNA profiling of Drosophila sensory organs precursor cells (SOP/pI) compared with neighbouring epithelial cells. Two-condition experiment, SOP/pI vs. epithelial cells from animals at similar developmental age.
2010-06-24 | E-GEOD-18615 | biostudies-arrayexpress
Project description:RNA profiling of Drosophila sensory organs precursor cells (SOP/pI) compared with neighbouring epithelial cells.
2010-02-19 | GSE18615 | GEO
Project description:Forty seven healthy HK-Chinese subjects between ages 18-30 were recruited. Subjects need to pass the McMonnies Questionnaire prior to the data collection. Visual functions and anterior ocular health were first assessed. One hour later, the subjects’ tear osmolalities were tested by the TearLab Osmometer. Tear samples were then collected by disposable microcapillary tubes. TripleTOF 6600 Mass Spectrometer was used to analyze the tear protein components.
2019-09-11 | PXD011864 | Pride
