Project description:We investigated the heterogeneous cell populations composing Bovine Intervertebral Discs (IVDs) through single cell RNA sequencing technologies. The assay sequenced over 14,000 cells composing 5 bovine discs from 3 unique bovine tails. Through both established and custom analysis pipelines, we characterize cell heterogeneity between populations of Nucleus Pulposus and Annulus Fibrosus cells. We further characterize populations of Endothelial, Muscle, Immune, and Notochord.
Project description:The widespread adoption of single-cell proteomics (SCP) in biology has been limited by complex workflows and reliance on specialized instrumentation. Here we present EasySCP, a high-throughput and lossless method that integrates FACS-based single-cell sorting, an all-in-one, single-step digestion process in 384-well plates, and sensitive mass spectrometry. EasySCP identifies nearly 5,000 proteins from individual HEK293 cell. Applied to murine liver, EasySCP achieved spatially resolved proteomics profiling of hepatocytes zonation, detecting an average of 3,500 proteins per hepatocyte and uncovering zonation patterns for 3,277 out of 5,267 proteins, representing unprecedented depth and coverage in single-cell liver proteomics. Building on 215 conserved zonation markers, we further developed hepatocyte spatial status score (HSS) that enables accurately reconstruct liver zonation across single-cell and spatial multi-omics datasets. Together, our study introduces EasySCP, a broadly accessible tool for dissecting cellular heterogeneity at single-cell proteomics resolution in both healthy and disease states, effectively bridging the gap between transcriptomics and functional proteomics.
Project description:The widespread adoption of single-cell proteomics (SCP) in biology has been limited by complex workflows and reliance on specialized instrumentation. Here we present EasySCP, a high-throughput and lossless method that integrates FACS-based single-cell sorting, an all-in-one, single-step digestion process in 384-well plates, and sensitive mass spectrometry. EasySCP identifies nearly 5,000 proteins from individual HEK293 cell. Applied to murine liver, EasySCP achieved spatially resolved proteomics profiling of hepatocytes zonation, detecting an average of 3,500 proteins per hepatocyte and uncovering zonation patterns for 3,277 out of 5,267 proteins, representing unprecedented depth and coverage in single-cell liver proteomics. Building on 215 conserved zonation markers, we further developed hepatocyte spatial status score (HSS) that enables accurately reconstruct liver zonation across single-cell and spatial multi-omics datasets. Together, our study introduces EasySCP, a broadly accessible tool for dissecting cellular heterogeneity at single-cell proteomics resolution in both healthy and disease states, effectively bridging the gap between transcriptomics and functional proteomics.
Project description:We combined the Single-probe single cell MS(SCMS) experimental technique with a bioinformatics software package, SinCHet-MS (Single Cell Heterogeneity for Mass Spectrometry), to characterize changes of tumor heterogeneity, quantify cell subpopulations, and prioritize the metabolite biomarkers of each subpopulation.
Project description:The widespread adoption of single-cell proteomics (SCP) in biology has been limited by complex workflows and reliance on specialized instrumentation. Here we present EasySCP, a high-throughput and lossless method that integrates FACS-based single-cell sorting, an all-in-one, single-step digestion process in 384-well plates, and sensitive mass spectrometry. EasySCP identifies nearly 5,000 proteins from individual HEK293 cell. Applied to murine liver, EasySCP achieved spatially resolved proteomics profiling of hepatocytes zonation, detecting an average of 3,500 proteins per hepatocyte and uncovering zonation patterns for 3,277 out of 5,267 proteins, representing unprecedented depth and coverage in single-cell liver proteomics. Building on 215 conserved zonation markers, we further developed hepatocyte spatial status score (HSS) that enables accurately reconstruct liver zonation across single-cell and spatial multi-omics datasets. Together, our study introduces EasySCP, a broadly accessible tool for dissecting cellular heterogeneity at single-cell proteomics resolution in both healthy and disease states, effectively bridging the gap between transcriptomics and functional proteomics.
Project description:The widespread adoption of single-cell proteomics (SCP) in biology has been limited by complex workflows and reliance on specialized instrumentation. Here we present EasySCP, a high-throughput and lossless method that integrates FACS-based single-cell sorting, an all-in-one, single-step digestion process in 384-well plates, and sensitive mass spectrometry. EasySCP identifies nearly 5,000 proteins from individual HEK293 cell. Applied to murine liver, EasySCP achieved spatially resolved proteomics profiling of hepatocytes zonation, detecting an average of 3,500 proteins per hepatocyte and uncovering zonation patterns for 3,277 out of 5,267 proteins, representing unprecedented depth and coverage in single-cell liver proteomics. Building on 215 conserved zonation markers, we further developed hepatocyte spatial status score (HSS) that enables accurately reconstruct liver zonation across single-cell and spatial multi-omics datasets. Together, our study introduces EasySCP, a broadly accessible tool for dissecting cellular heterogeneity at single-cell proteomics resolution in both healthy and disease states, effectively bridging the gap between transcriptomics and functional proteomics.
Project description:We have applied single cell RNA sequencing (scRNA-seq) as an unbiased transcriptomics to characterize aortic immune cells in atherosclerosis. The scRNA-seq analysis revealed macrophage heterogeneity at the single-cell level in mouse atherosclerotic aorta.
