Hints from Honeycomb: How Does Single Cell RNA Sequencing Work?

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Generating a comprehensive gene expression profile for a sample type of interest is essential for understanding its underlying biology. Two primary methods of RNA sequencing (RNAseq) are:

  • Bulk RNAseq, which shows the gene expression for a sample as a whole, providing an average view of everything that is being transcribed in all of the cells.
  • Single-cell RNAseq (scRNAseq), which allows researchers to determine the distinct gene expression profiles of individual cell-types within their sample.

Imagine RNAseq as a bowl of fruit being blended into a smoothie. Bulk analysis is like the smoothie; the taste is a blend of all of the individual fruits present. Single-cell analysis is like the examination of each individual fruit from the bowl before the smoothie is made, allowing for the identification of types of fruit present, their frequencies, and unique properties. This increase in resolution has changed biology, providing information for individual cell-types or even cell states that may have been lost before.

How can the smoothie analogy be extrapolated to real-life applications? As an example, identifying which cells within a sample are disease-causing (pathogenic) can be challenging, despite differences in transcriptional profiles. While pathogenic genes-of-interest may be detected by bulk RNAseq, the identity of the cells these genes are associated with is difficult to discover. Additionally, biologically important genes may be hidden because they are expressed by cell-types that make up a minority of the sample and therefore fall below the average level of detection. Single-cell RNAseq overcomes these limitations in detection, disentangling the unique gene expression profile of each cell-type within a sample and revealing differences in transcription that might otherwise have been masked by the rest of the population.

Single-cell genomics is quickly revolutionizing the way we uncover biological complexities in the world around us. In the next post, we’ll do a deeper dive into the benefits of using single-cell RNAseq technology.

Learn about the HIVE™ complete scRNA-seq solution.

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