Single cell sequencing

author image

James Ashmore   |     |  Read Time 2 mins


This week I was thinking about how maps were drawn in the ancient world. If I were given the challenge of drawing a map of my local area without using today’s technology, how would I do it? Would I walk around sketching my surroundings with a pencil and paper? Would I try to be clever and use a standard length of string to measure the distance between features on my street? This question led me to reading about the long and fascinating history of cartography – the art and science of graphically representing a geographical area, usually on a flat surface such as a map or chart.

It's hard to overstate how effective maps are at displaying complex information in a simple way. They allow us to comprehend the shapes and sizes of areas, the location of features, and the distances between places. It comes as no surprise then that life science researchers have seized upon the idea and started making maps of their own. However, these maps don’t describe geographical areas, instead, they illustrate the cellular landscape of tissues from a single organism. These maps are probably better described as atlases, given they aim to describe the entire organism akin to the earth’s globe.

Quickly going back to the question at the beginning, how did the ancient world create maps? It turns out a mathematical method called triangulation allowed them to precisely determine the location of a point using an array of different tools. In fact, this method is still widely used today, albeit with the help of more advanced technology like satellites. So, what about these maps life science researchers are producing? What tools and methods do they use? The advent of single-cell gene expression technology allowed researchers to isolate and record the gene expression profile of millions of individual cells. Using machine learning algorithms, cells can be placed on a so-called map based on the similarity of their expression profiles. Once drawn, biologists and other domain experts can annotate and curate the atlas to produce a highly informative visualization of the cellular landscape of an organism.


So, what sorts of questions can we answer with an expression atlas? Really, the number of questions is only limited by two things: the ingenuity of the researcher and the quality of the data. Usually, we are interested in cataloguing all the different types of cells, measuring what genes are uniquely expressed in one cell type but not the other, modelling the developmental relationship between cells, and identifying what genes or cells are disrupted by a given disease state. A fantastic example of the insights which can be achieved with this technology comes from the Human Cell Atlas project, a herculean effort to chart the cell types in the healthy body across time from development to adulthood and eventually to old age. See below for an example of an expression atlas taken from the project website.


If you’re interested in creating an expression atlas for a tissue or disease state you’re studying, get in touch with us by email at info@zifornd.com and we can discuss the design and implementation.

James Ashmore
Lead Bioinformatician (Europe)