Aug 30, 2016

From fruit smoothie to fruit salad: revealing the individual cell types that cause disease

Fred 10x

You’re sitting at home drinking a smoothie and you notice something is off. Maybe the flavor isn’t quite right, or the color looks a bit strange and you think to yourself: "was any of the fruit I put in rotten, or moldy?" Maybe it was the strawberries, or the bananas?  Yes, that must be it.  But, in reality, it’s hard to tell from your homogenous smoothie drink. A similar problem exists when researchers examine cancerous or other diseased tissues as a single, homogenous mixture, when really they are comprised of many individual cell types. In order to know which fruit in the smoothie went bad, we need to look at the individual fruit before they went in the blender; to know which cells are driving a cancer we must examine the individual tumor cell populations. Elucidating these cancer cell types and understanding how and why certain types become cancerous is a critical goal in the modern age of medicine.

In recent years many technologies have been developed to look at individual cells at both the DNA and mRNA level to better understand what cell types are present in a tissue and how their malfunction can lead to disease. These approaches typically involve plate based or microfluidic methods; however, these methods are commonly limited in throughput (plate-based) or have have cell selection bias on the basis of cell size (microfluidic capture methods). In order to discover rare populations of cells in highly heterogeneous tissues however, requires unbiased profiling of thousands of single cells coupled with robust computational pipelines, something that has been lacking in the field…until now.

With the release of the 10x Genomics Chromium™ Single Cell 3’ Solution, researchers can now profile 10,000’s of individual cells in an unbiased fashion using the Chromium platform to generate single-cell barcoded, sequencing-ready libraries that can be run on most Illumina sequencers.  After sequencing, Cell Ranger software transforms the barcoded sequencing data into files ready for single cell expression analysis and visualization.  The Chromium platform has been demonstrated to work on a wide range of cell types, from PBMCs to intestinal epithelium, providing researchers a high-resolution picture of the cell types and tissues commonly involved in cancer and other disease states.

For more information about this latest breakthrough in single cell sequencing technology and to see how the 10x Chromium platform can provide novel insights into your biological questions:

  • Read the new Chromium Single Cell 3’ Solution Application Note 
  • Download Single Cell datasets
  • Learn more about the Chromium Single Cell Software Suite including Cell Ranger analysis pipelines and R kit