Methods utilizing single cell genetic data for cell population analysis and applications thereof
AssigneeThe Board of Trustees of the Leland Stanford Junior University
InventorsAaron M. Newman, Gunsagar S. Gulati, Michael F. Clarke, Shaheen Shabbir Sikandar
Life of this patent
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Abstract
Processes to infer stemness, cell lineage, and/or differentiation status are provided. In some instances, single cell RNA sequencing is used to infer a cell's stemness, cell lineage, and/or differentiation status. In some instances, a collection of cells is ordered based on each cell's differentiation status.
Claims27
A method to infer a differentiation status of a plurality of cells, comprising:
- obtaining single cell sequencing results of a plurality of cells, wherein the sequencing was performed on each single cell individually and each cell's sequencing result includes the cell's gene expression;
- for each cell of the plurality of cells, determining the expression level of a set of genes from the single cell sequencing results, wherein the set of genes are genes having an expression pattern that have been determined to be correlated with gene counts;
- and
- determining the differentiation status of each cell of the plurality of cells relative to each other based on each cell's expression of the set of genes that are most correlated with gene counts, wherein cells having lower gene counts, as determined by the correlative gene expression, are more differentiated than cells having higher gene counts.
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A method to infer a differentiation status of a plurality of cells, comprising:
- obtaining single cell sequencing results of a plurality of cells, wherein the sequencing was performed on each single cell individually and each cell's sequencing result includes the cell's gene expression;
- for each cell of the plurality of cells, determining a total number of genes expressed within that cell as determined from the single cell sequencing results;
- determining the differentiation status of each cell of the plurality of cells relative to each other based on the total number of genes expressed within each cell, wherein cells having lower gene counts are more differentiated than cells having higher gene counts.
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A method to identify quiescent stem cells within a plurality of cells, comprising:
- obtaining single cell sequencing results of a plurality of cells, wherein the sequencing was performed on each single cell individually and each cell's sequencing result includes the cell's gene expression;
- for each cell of the plurality of cells, determining the expression level of a set of genes from the single cell sequencing results, wherein the set of genes are genes that are most correlated with gene counts;
- for each cell of the plurality of cells, determining the total RNA content of each single cell;
- identifying stem cells by determining the differentiation of each cell of the plurality of cells relative to each other;
- wherein differentiation status is based on each cell's expression of the set of genes that are most correlated with gene counts, wherein cells having lower gene counts, as determined by the correlative gene expression, are more differentiated than cells having higher gene counts;
- and
- identifying quiescent cells within the identified stem cells by determining the quiescent status of the plurality of cells relative to each other;
- wherein quiescent status is based on the total RNA content, wherein cells having lower RNA content are more quiescent that cells having higher RNA content.
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Dependencies are inferred from the claim text.