How to analyze scRNA-seq, scATAC-seq and Multiome data
In contrast to bulk RNA-seq, which produces an average gene expression profile for all cells within a sample by measuring the transcriptome of the entire sample, single-cell RNA-seq (scRNA-seq) produces transcriptomics measurements for each of the many thousands of individual cells within the sample. This allows for the effective identification and characterization of subpopulations of cells within the sample.
Similarly, single-cell ATAC-seq (scATAC-seq) measures chromatin accessibility on a single-cell level, enabling the identification of subpopulations of cells with different open chromatin profiles and distinct gene expression regulation profiles.
Several companies offer quality scRNA-seq and scATAC-seq services, but 10X Genomics has gained popularity as a leading provider due to their advanced technologies, proven quality standards, reasonable cost, and advanced data processing and analysis systems.
While scRNA-seq and scATAC-seq can be conducted on the same sample to provide both gene expression and gene regulatory information, this information is not "matched". This means that if we identify a subpopulation of cells with an interesting expression profile in the scRNA-seq experiment, we do not have information about how this subpopulation of cells is regulated or whether it represents a homogenous subpopulation in terms of regulatory profiles. Similarly, if we identify a subpopulation of cells with an interesting open chromatin profile using scATAC-seq, we have no information about the expression profiles of those cells or whether they have uniform expression profiles.
Recently, 10X Genomics developed a new experimental protocol called Multiome to address this problem. In a Multiome experiment, both the transcriptome and chromatin accessibility are measured on the same cell, allowing for simultaneous and joint interrogation of gene expression and gene regulatory mechanisms.
- Intro to scRNA-seq, scATAC-seq and Multiome
- Steps to take to analyze scRNA-seq, scATAC-seq and Multiome data
- Significance of single-cell analysis
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