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ShareScore release 0.9.0
Dataset results
26 results for “CosMx”
Spatial profiling of benign and malignant melanocytic tumors via RNA-SMI (CosMx)
<p>Melanoma clinical outcomes emerge from incompletely understood genetic mechanisms operating within the tumor and its microenvironment. Here, we utilized single-cell RNA-based spatial molecular imaging (RNA-SMI) in patient-derived archival tumors to reveal clinically relevant markers of malignancy progression and prognosis. We examined spatial gene expression of 203,472 cells inside benign and malignant melanocytic neoplasms, including melanocytic nevi, primary invasive and metastatic melanomas. Algorithmic cell clustering paired with intratumoral comparative 2D-analyses visualized synergistic, spatial gene signatures linking cellular proliferation, metabolism, and malignancy, validated by protein expression. Metastatic niches included upregulation of CDK2 and FABP5, which independently predicted poor clinical outcome in 473 melanoma patients via Cox regression analysis. More generally, our work demonstrates a framework for applying single-cell RNA-SMI technology toward identifying gene regulatory landscapes pertinent to cancer progression and patient survival.</p>
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment - Nanostring CosMx SMI Data
<p>Data export from Nanostring CosMx SMI, directly from Nanostring, in Seurat Object format for use in R. Clear cell renal cell carcinoma and papillary renal cell carcinoma were profiled before and after exposure to immunotherapy, with and without sarcomatoid features in clear cell tumors. Each tumor had a field of view in the stromal compartment and field of view in the tumor compartment.</p> <p>For appropriate clinical information associated with this study, please contact Dr. Brandon Manley.</p>
CosMx Spatial transcriptome dataset of human gastric mucosa
<p>This dataset contains the spatial transcriptome dataset of human gastric mucosa obtained by CosMx</p> <p>A zip file contains the following folders and files:</p> <p><strong>Folders</strong></p> <p>- CellComposite folder: the composite immunofluorescent images of each FOV.</p> <p>- CellLabels folder: the cell definitions images for each FOV determined during cell segmentation.</p> <p>- CellOverlay folder: the cell boundary images for each FOV determined during cell segmentation.</p> <p>- CompartmentLabels folder: the subcellular compartment images for each FOV determined during cell segmentation. The compartment types are as follows: 0. Extracellular, 1. Nuclear, 2. Membrane, 3. Cytoplasmic</p> <p>- RawMorphologyImages folder: raw morphological TIF images for each FOV</p> <p> </p> <p><strong>Files</strong></p> <p>- Run5458_{sample_name}_exprMat_file.csv: cell expression matrix.</p> <p>- Run5458_{sample_name}_fov_positions_file.csv: each FOV relative position within global structure.</p> <p>- Run5458_{sample_name}_metadata_file.csv: the metadata of each cell.</p> <p>- Run5458_{sample_name}_tx_file.csv: the transcript file for each target gene and its position.</p> <p>- Run5458_{sample_name}-polygons.csv: the segmentation polygon file.</p> <p> </p> <p><strong>Citation</strong></p> <p>If you use this dataset for your research, please cite our paper.</p> <p>Ayumu Tsubosaka, Daisuke Komura, Miwako Kakiuchi, Hiroto Katoh, Takumi Onoyama, Asami Yamamoto, Hiroyuki Abe, Yasuyuki Seto, Tetsuo Ushiku, Shumpei Ishikawa, Stomach encyclopedia: Combined single-cell and spatial transcriptomics reveal cell diversity and homeostatic regulation of human stomach, Cell Reports, Volume 42, Issue 10, 2023, 113236, https://doi.org/10.1016/j.celrep.2023.113236.</p>
Spatial profiling of benign and malignant melanocytic tumors via RNA-SMI (CosMx)
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Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples [CosMx]
GEO Series GSE299786. Homo sapiens. 4 samples. Type: Other.
Microglia - astrocyte cross-talk in the amyloid plaque niche of an Alzheimer’s disease mouse model as revealed by spatial transcriptomics (CosMx)
GEO Series GSE263791. Mus musculus. 2 samples. Type: Other.
Nanostring CosMx 6,000-plex RNA profiling of human kidney nephrectomy specimens
GEO Series GSE282059. Homo sapiens. 1 samples. Type: Expression profiling by array; Other.
In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment [Nanostring CosMx]
GEO Series GSE310352. Homo sapiens. 8 samples. Type: Other.
Comparison of CosMx and GeoMx profiling performed on the same human kidney tissues [CosMx]
GEO Series GSE278766. Homo sapiens. 1 samples. Type: Other.
STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging [CosMx Spatial]
GEO Series GSE290466. Homo sapiens. 92 samples. Type: Other.
6K-plex RNA CosMx data from DLBCL sections.
GEO Series GSE289194. Homo sapiens. 83 samples. Type: Other.
Cosmx Spatial Analysis of whole brain slices and ventral pallidum
GEO Series GSE292791. Mus musculus. 1 samples. Type: Other.
Single-cell single-molecule spatial transcriptomics using CosMx on colectomy specimens collected during Pouch surgery in IBD patients.
GEO Series GSE283625. Homo sapiens. 8 samples. Type: Other.
Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - CosMx Data
GEO Series GSE308146. Homo sapiens. 4 samples. Type: Other.
Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer [CosMx]
GEO Series GSE277782. Homo sapiens. 7 samples. Type: Other.
Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome [Nanostring CosMx SMI spatial transcriptomics]
GEO Series GSE297091. Homo sapiens. 1 samples. Type: Other.
Programmed cell death-1 receptor deficiency enhances CD30+ T regulatory cell function in Melanoma [Murine NanoString CosMx SMI]
GEO Series GSE273530. Mus musculus. 1 samples. Type: Other.
IBD CosMx NanoString data from colonic mucosa
GEO Series GSE234713. Homo sapiens. 9 samples. Type: Other.
Nanostring CosMx 980-plex RNA profiling of human kidney biopsy and nephrectomy
GEO Series GSE253439. Homo sapiens. 4 samples. Type: Other.
Thyroid Hormone Promotes Fetal Neurogenesis [CosMx]
GEO Series GSE305978. Homo sapiens. 1 samples. Type: Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.