Matthew Ruffalo

A collection of datasets from Publication: HuBMAP Data Portal: A Resource for Multimodal Spatial and Single-Cell Data of Healthy Human Tissues

Morgan L. Turner, Thomas Chris Smits, Tiffany Sun Liaw, Brendan Honick et autres

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SenNet Portal: Build, Optimization and Usage

K. Borner, Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo et autres

Cellular senescence is a hallmark of aging and a driver of functional decline across tissues, yet its heterogeneity and context dependence have limited systematic study. The Common Fund's Cellular Senescence Network (SenNet) Program addresses this challenge by generating multimodal, multi-tissue datasets that …

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SPRM: spatial process and relationship modeling for multiplexed images

Ted Zhang, Haoran Chen, Young Je Lee, Matthew Ruffalo et autres

Motivation: There has been tremendous recent growth both in technologies for measurement of many different markers in the same tissue and in resulting datasets (especially from projects such as HuBMAP and the Human Cell Atlas). Analysis of images in these datasets is …

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Light Sheet

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

Light Sheet Fluorescence Microscopy (LSFM) is a volumetric imaging technique that illuminates a sample with a thin plane of laser light perpendicular to the detection axis, enabling rapid, high-resolution 3D imaging with minimal photobleaching and phototoxicity. By exciting only the in-focus plane, …

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MPLEx

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

Multi-Phase Liquid Extraction (MPLEx) is a simple, rapid, and robust sample preparation protocol for integrated multi-omics analysis from diverse biological sample types, including environmental, in vitro, and clinical specimens. Based on a modified Bligh-Dyer solvent extraction, MPLEx simultaneously partitions lipids, metabolites, and …

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Olink

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

Olink is a high-throughput protein biomarker discovery platform that uses Proximity Extension Assay (PEA) technology to simultaneously measure the concentration of thousands of human proteins from small sample volumes. Pairs of antibodies conjugated to complementary DNA oligonucleotides bind the same target protein; …

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Cell DIVE

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

Cell DIVE is a highly multiplexed fluorescence imaging assay that enables quantification of more than 60 protein biomarkers within a single, intact fixed tissue section. The workflow consists of iterative cycles of antibody staining, multi-channel fluorescence imaging, and chemical dye inactivation, with …

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DBiT-seq

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq) simultaneously maps mRNA transcripts and protein expression within intact tissue sections using microfluidic co-delivery of DNA barcodes. Spatially indexed barcodes are deposited in a deterministic grid pattern onto the tissue, capturing both RNA …

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SIMS

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

Secondary Ion Mass Spectrometry (SIMS) is an analytical surface technique that characterizes the elemental and molecular composition of solid surfaces and thin films by bombarding the specimen with a focused primary ion beam, causing secondary ions to be sputtered from the surface …

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COMET

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

The COMET assay (single-cell gel electrophoresis) is a technique that measures DNA strand breaks and damage within individual cells. Cells are embedded in agarose gel, lysed, and subjected to electrophoresis; damaged DNA fragments migrate out of the nucleus to form a 'comet …

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Visium (with probes)

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

Visium with probes (via 10x Genomics Visium CytAssist) is a probe-based spatial transcriptomics approach that combines histological imaging with targeted transcriptomic profiling in the spatial context of intact tissue. Target-specific hybridization probes capture RNA sequences of interest from the tissue; the CytAssist …

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CosMx Transcriptomics

Stephen Fisher, Josef Hardi, Richard S. Morgan, Mark A. Musen et autres

CosMx Transcriptomics is a high‑plex in situ RNA imaging technology that maps gene expression within intact FFPE or fresh‑frozen tissue at single-cell and subcellular resolution using single‑molecule detection and cyclic fluorescence readout. Tissue sections are hybridized with target-specific probe sets and imaged …

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