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Multi-modal single cell RNA assays capture RNA content as well as other data modalities, such as spatial cell position or the electrophysiological properties of cells. Compared to dedicated scRNA-seq assays however, they may unintentionally capture RNA from multiple adjacent cells, exhibit lower RNA sequencing depth compared to scRNA-seq, or lack genome-wide RNA measurements. We present scProjection, a method for mapping individual multi-modal RNA measurements to deeply sequenced scRNA-seq atlases to extract cell type-specific, single cell gene expression profiles. We demonstrate several use cases of scProjection, including the identification of spatial motifs from spatial transcriptome assays, distinguishing RNA contributions from neighboring cells in both spatial and multi-modal single cell assays, and imputing expression measurements of un-measured genes from gene markers. scProjection therefore combines the advantages of both multi-modal and scRNA-seq assays to yield precise multi-modal measurements of single cells.
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Assessing Human Articular Cartilage Transcriptome Layers with RNA Sequencing
Osteoarthritis, a chronic disease, remains an issue for adults that causes cartilage degradation within a joint . According to the Centers forDisease Control and Prevention (2023), over 32.5 million adults in the US are affected by osteoarthritis (OA). In this study we seek tounderstand the connection between tissue engineering and genetics to regenerate human articular cartilage (hAC). We purpose to validatea protocol for RNA isolation and characterize the transcriptome of hAC in a tri-layer fashion via bulk RNA sequencing (bulk-RNA-seq).Additionally, we aim to analyze the transcriptome of normal articular cartilage in comparison to the hAC chemical composition and physicalproperties. We are relating these properties to the tri-layers of hAC through histological staining with Safranin O—Fast green and imagingwith differential interference contrast (DIC) microscopy. We are relating these properties to superfic ial, middle, and deep zone with acryotome procedure, RNA extracted, and qualified by Bioanalyzer. Next, we generate bulk RNA sequencing of hAC layer-by-layer andcompare results to early passaging of Mesenchymal Stromal Cells (MSC) and tissues intended for Matrix-Induced Autologous ChondrocyteImplantation (MACI). We will use differential gene expression (DE) analysis by DESeq2 R package software for bulk-RNA-seq. The resultwill be interpreted in terms of differentiation from MSCs to gene expression patterns of tri-layer hAC. We will report on development andvalidation of protocols for isolating cells and their subsequent characterization with application in regenerating the tri-layered hACtranscriptome stimulatory bioreactors used in our laboratory and corresponding properties of the extracellular matrix (ECM)
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- Award ID(s):
- 2225528
- PAR ID:
- 10639224
- Publisher / Repository:
- American Institute of Chemical Engineering
- Date Published:
- Format(s):
- Medium: X
- Location:
- San Diego, CA
- Sponsoring Org:
- National Science Foundation
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