Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial Transcriptomics of the human musculotendinous unit, the myotendinous junction

ABSTRACT: Identification of cell types in the interphase between muscle and tendon by Visium Spatial Transcriptomics of four human semitendinous muscle-tendon biopsies. Cell types identified by single nuclei RNA seq on similar tissue were localized in situ with the use of Spatial Transcriptomics.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Peter Schjerling

PROVIDER: E-MTAB-12530 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

GeoMx digital spatial profiling on enthesis biopsies from psoriatic arthritis patients before and after treatment with secukinumab

Project description:Enthesitis, a hallmark of psoriatic arthritis (PsA), reflects the interplay between mechanical stress and immune dysregulation at tendon-bone interfaces. We aimed to investigates the cellular and molecular responses in entheseal tissues following IL-17A inhibition in patients with active PsA. To identify changes in the mesenchymal and non-mesenchymal compartments pre- and post-treatment, we performed GeoMx spatial transcriptomics on CD45+ and vimentin+ cells on entheseal biopsies from 6 PsA patients before and after treatment with secukinumab.

2025-12-31 | E-MTAB-15134 | biostudies-arrayexpress

Single-nucleus RNA-seq of the human musculotendinous unit, the myotendinous junction

Project description:Identification of cell types in the interphase between muscle and tendon by single-nuclei RNA-seq of three human semitendinous muscle-tendon biopsies. With special focus on the myotendinous junction specific myonuclei, transcripts were identified and confirmed to myotendinous junction with immunofluorescence.

2023-03-02 | E-MTAB-12529 | biostudies-arrayexpress

GeoMX spatial transcriptomics of diffuse pleural mesothelioma: impact of CDKN2A deletion

Project description:We compared GeoMX spatially resolved gene expression profiles of diffuse pleural mesothelioma (DPM) samples with or without somatic CDKN2A deletion. 5 CDKN2Adel and 4 WT DPM samples were analyzed. A total of 202 Areas Of Illumination (AOIs) were transcriptionally profiled, of which 140 Sarcomatoid-AOIs (S-AOIs) and 62 Epithelioid-AOIs (E-AOIs). Collectively, 97 AOIs belonged to WT DPM and 105 to CDKN2Adel DPMs.Profiling was performed using the GeoMx™Digital Spatial Profiler with Cancer Transcriptome Atlas panel.

2026-05-01 | E-MTAB-15378 | biostudies-arrayexpress

Vascular niches as the primary hotspots for cardiac aging

Project description:Aging is a major, yet unmodifiable, risk factor for cardiovascular disease, leading to vascular alterations, increased cardiac fibrosis, and inflammation, all of which contribute to impaired cardiac function. To investigate the spatial impact of aging, we applied an integrative approach combining single-nucleus RNA sequencing and spatial transcriptomics in 12-week-old and 18-month-old mice. We systematically mapped the aging heart and identified larger vessel-associated niches as key hotspots for activated macrophages and fibroblasts in aged hearts. These niches, surrounding arteries, were also enriched in senescent cells. Our findings suggest that the microenvironment around the vasculature is particularly susceptible to age-related changes and serves as a primary site for inflammation-driven aging so called \"inflammaging\". This study provides new insights into how aging reshapes cardiac cellular architecture, highlighting vessel-associated niches as potential therapeutic targets for age-related cardiac dysfunction.

2025-10-31 | E-MTAB-14947 | biostudies-arrayexpress

Spatial transcriptomics of 8 whole opisthosomas samples from adult female L. sclopetarius spiders

Project description:This dataset comprises spatial transcriptomics of 8 whole opisthosomas samples isolated from adult female L. sclopetarius spiders.

2024-06-01 | E-MTAB-14082 | biostudies-arrayexpress

Spatial transcriptomics of skin biopsies from patients with cutaneous T cell lymphoma (CTCL)

Project description:CTCLs are a group of non-Hodgkin lymphomas, with non-aggressive forms (Mycosis fungoides (MF)) initially presenting with features of cutaneous eczema or psoriasis, posing a challenge for clinical and histological diagnosis. Using spatial transcriptomics, we hope to delineate the molecular signatures of CTCL to provide novel avenues for diagnostics and therapies.

2024-04-01 | E-MTAB-13614 | biostudies-arrayexpress

Spatial Multi-Omics Identifies Early Synaptic Pruning and Context-Specific Dopaminergic Vulnerability in Synucleinopathies

Project description:Parkinson’s disease (PD) is characterized by degeneration of dopaminergic neurons in the substantia nigra pars compacta, but the molecular events preceding neuronal loss remain unclear. Here, we combine spatial transcriptomics, spatial proteomics, and α-synuclein (αSyn) seed amplification assays to profile post-mortem midbrain tissue from controls, incidental Lewy body disease (iLBD), PD, Alzheimer’s disease (AD), and AD with Lewy body pathology (AD+LBP). We find that αSyn seeding activity correlates with dopaminergic neuron loss in PD-spectrum cases but not in AD-associated LBP, indicating disease-context dependent relationships between αSyn pathology and neurodegeneration. In iLBD, before overt substantia nigra Lewy pathology or detectable αSyn aggregation, we detect increased expression of the complement component C1QC together with loss of inhibitory synaptic markers. These findings support early complement-associated remodeling of inhibitory synapses as a potential pathogenic event preceding overt αSyn aggregation and neuronal degeneration in PD.

2026-06-09 | PXD062998 | Pride

GBM-Space: Spatial Transcriptomic Profiling of Glioblastoma (10x Genomics - Visium)

Project description:Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This submission contains the Space Ranger processed outputs from Visium spatial transcriptomic sequencing (10x Genomics), including paired high-resolution H&E tissue images. We also provide an integrated single cell and spatial dataset across 97 Visium sections, including gene expression, cell state abundances, and histopathological annotations.

2026-06-12 | E-MTAB-17164 | biostudies-arrayexpress

GeoMX spatial transcriptomic on biphasic Malignant Pleural Mesothelioma

Project description:We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morpho-logical evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler and Cancer Transcriptome Atlas to compare epithelioid and sarcomatoid components transcriptional profile and reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions.

2023-12-07 | E-MTAB-13043 | biostudies-arrayexpress

Basal-like breast cancer stimulates MUC1 to support an epithelial/mesenchymal hybrid state and survive radiotherapy

Project description:We employed high-throughput sequencing with spatial resolution in the WAP-T mouse model of basal-like breast cancer (BLBC) to investigate the transcriptomic response to radiation therapy (RT). Our analysis revealed a distinct spatial pattern of gene expression (10X visium platform), with irradiated BLBC tumors exhibiting a strong enrichment of epithelial genes and a hybrid epithelial/mesenchymal (E/M) state. Notably, MUC1 expression was upregulated in response to RT, suggesting its role as a key driver of cell survival. These findings provide new insights into the spatial transcriptomic landscape of BLBC under RT and highlight the potential of MUC1 as a therapeutic target or prognostic marker for optimizing patient response to RT.

2026-03-19 | E-MTAB-15010 | biostudies-arrayexpress

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