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MetabolomicsOrganotypic microfluidic breast cancer model reveals starvation-induced spatial-temporal metabolic adaptations
BACKGROUND: Ductal carcinoma in situ (DCIS) is the earliest stage of breast cancer. During DCIS, tumor cells remain inside the mammary duct, growing under a microenvironment characterized by hypoxia, nutrient starvation, and waste product accumulation; this harsh microenvironment promotes genomic in...
2019-02-08 | MTBLS669 | MetaboLights
ProteomicsSpatial SILAC Regorafenib Treated Bottom-up Proteomic Analysis
Developing effective model systems to evaluate new potential chemotherapeutic reagents is critical. Three-dimensional cell cultures, such as spheroids, aid in bridging the gap between commonly used monolayer cell cultures and significantly more complex and expensive animal models. Spheroid model sys...
ORGANISM(S): Homo sapiens (Human) 
2024-08-09 | PXD038958 | Pride
Spatial silac Regorafenib Spheroids 
GenomicsSpatiotemporal proteomics reveals dynamic antiparallel gradients shaping signalling waves [Spatial RNAseq]
Spatiotemporal proteomics reveals dynamic antiparallel gradients shaping signalling waves [Spatial RNAseq]
PRJNA1299793 | ENA
ProteomicsSingle-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture
Understanding protein distribution patterns across tissue architecture is crucial for deciphering organ function in health and disease. Here, we applied single-cell Deep Visual Proteomics to perform spatially-resolved proteome analysis of individual cells in native tissue. We built a robust framewor...
ORGANISM(S): Homo sapiens (Human) 
2025-12-19 | PXD062231 | Pride
Deep visual proteomics Single cell proteomics Spatial protein gradients Fibrosis Human liver zonation 
TranscriptomicsSpatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons
Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-c...
ORGANISM(S): Mus musculus 
2016-01-05 | E-GEOD-67403 | biostudies-arrayexpress
TranscriptomicsTranslation State Array Assay for C elegans IFE-1-dependent mRNAs
Relative polysomal loading changes for wild type (N2) versus ife-1(bn127) C. elegans strains Strain ife-1(bn127) is null for the gene encoding one of five eIF4E isoforms in the worm, IFE-1. Only this isoform associates with P granules. Resolution of translating and non-translating mRNAs from WT and...
ORGANISM(S): Caenorhabditis elegans 
2016-01-07 | E-GEOD-74459 | biostudies-arrayexpress
ProteomicsAn ultrasensitive spatial tissue proteomics workflow exceeding 100 proteomes per day
Achieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing, chromatography, and MS acquisition. Here, we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients (20, ...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2026-01-05 | PXD069877 | Pride
ProteomicsSpatial proteomics of the diaphragm
The thoracic diaphragm is a vital organ for respiration and morphological studies of the diaphragm have provided a detailed view of its architecture consisting of parallel muscle fibers, a central ring of neuromuscular junction (NMJ) units and a muscle-tendon transition area. Although immunohistoche...
ORGANISM(S): Mus musculus (Mouse) 
2026-09-22 | PXD054352 | Pride
Nmj Diaphragm Spatial proteomics Mtj 
UnknownModeling robustness tradeoffs in yeast cell polarization induced by spatial gradients.
Not available
S-EPMC3021495 | biostudies-literature
ProteomicsSpatial proteomics of skeletal muscle using thin cryosections reveals metabolic adaption at the muscle-tendon transition zone
Morphological studies of skeletal muscle tissue have provided detailed insights into the architecture of muscle fibers, the surrounding cells, and the extracellular matrix. However, a spatial proteomics analysis of the skeletal muscle, including the muscle-tendon transition zone, is lacking. Here, w...
ORGANISM(S): Mus musculus (Mouse) 
2024-05-22 | PXD046596 | Pride
Mtj Skeletal muscle Spatial proteomics 
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