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Mapping alterations spatially and temporally during early stages of breast tumourigenesis

ABSTRACT: Mapping alterations spatially and temporally during early stages of breast tumourigenesis

PROVIDER: PRJNA294595 | ENA |

REPOSITORIES: ENA

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Mapping alterations spatially and temporally during early stages of breast tumourigenesis [aCGH]

Project description:Identifying genomic alterations that precede tumourigenesis of breast tumours will allow us to better understand tumour development and heterogeneity. In particular, by obtaining and profiling normal-epithelium samples at various distances from the tumour, we can draft both a spatial and temporal map of the genomic events and transcriptomic alterations that occur along the mammary duct (leading up to and including the tumour).

2017-11-02 | GSE72652 | GEO

Mapping alterations spatially and temporally during early stages of breast tumourigenesis [expression]

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Mapping alterations spatially and temporally during early stages of breast tumourigenesis

Project description:This SuperSeries is composed of the SubSeries listed below.

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DIURNAL RHYTHMS SPATIALLY AND TEMPORALLY ORGANIZE AUTOPHAGY

Project description:RAW spectrum files associated with "DIURNAL RHYTHMS SPATIALLY AND TEMPORALLY ORGANIZE AUTOPHAGY"

2019-01-15 | MSV000083314 | MassIVE

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Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation

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Temporally & Spatially-Resolved Microproteomics and MALDI MSI Lipidomic Analysis for Traumatic Brain Injury

Project description:Using an experimental TBI rat model of mild/moderate Controlled Cortical Impact (CCI) injury, we combined large-scale proteomics identification and relative quantification using Spatially-Resolved Microproteomics with MALDI MS Imaging of Lipids. Spatially by studying different regions in the brain post injury in a coronal view, with main focus on the injury site itself. Temporally by studying the acute and subacute phase post injury, including injured rat brains at 1 day, 3 days, 7 days, and 10 days post injury. Direct on-tissue micro-digestion followed by micoextraction from 1 mm2 surface area within the injured cortical tissue were subjected to LC-MS & MS/MS analysis using HR MS. In addition, several identified potential biomarkers within our study were used to stimulate dorsal root ganglion (DRG), astrocyte, and macrophage cell lines to obtain a better understanding of their role and contribution in the injury.

2019-06-19 | PXD011262 | Pride

Ion mobility-based sterolomics reveals spatially and temporally distinctive sterol lipids in the mouse brain

Project description:Aberrant sterol lipid metabolism is associated with physiological dysfunctions in the aging brain and aging-dependent disorders such as neurodegenerative diseases. There is an unmet demand to comprehensively profile sterol lipids spatially and temporally in different brain regions during aging. Here, we develop an ion mobility-mass spectrometry based four-dimensional sterolomics technology leveraged by a machine learning-empowered high-coverage library (>2000 sterol lipids) for accurate identification. We apply this four-dimensional technology to profile the spatially resolved landscapes of sterol lipids in ten functional regions of the mouse brain, and quantitatively uncover ~200 sterol lipids uniquely distributed in specific regions with concentrations spanning up to 8 orders of magnitude. Further spatial analysis pinpoints age-associated differences in region-specific sterol lipid metabolism, revealing changes in the numbers of altered sterol lipids, concentration variations, and age-dependent coregulation networks. These findings will contribute to our understanding of abnormal sterol lipid metabolism and its role in brain diseases.

2021-05-24 | MTBLS2457 | MetaboLights

A method for spatially and temporally resolved protein network interrogation in living cells

Project description:Cells operate through protein interaction networks organized in space and in time, but current methods to interrogate such biology typically resolve only one of these dimensions. Here, we describe a method to resolve both dimensions simultaneously using proximity labeling mediated by engineered ascorbic acid peroxidase (APEX). APEX has been used to label organelle proteomes with high temporal resolution, but its spatial resolution is generally thought to be limited because of its larger labeling radius. We describe an analytical pipeline, based on quantitative proteomics using spatial references, which overcomes this barrier. As proof-of-principle, we apply the methodology to interrogate protein interaction networks of G protein coupled receptors both temporally and spatially. Using this approach, we identify known binding partners as well as novel receptor regulators. Validating the methodology as a discovery tool, we demonstrate that two of these components drive ubiquitin-linked down-regulation of opioid receptors.

2017-03-03 | PXD005758 | Pride

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