- 'First, a scientist begins
with the perception of a problem.'
- Science is hard.
Scientists spend a lot of time
making guesses and having them be wrong.
- One of the big mysteries
of life itself is the cell and how cells work—
and many of the most prevalent diseases
can be traced back to disorders of the cell.
- There is an ambitious, globe-spanning effort
underway to create cell atlases:
detailed maps of all the cells in a human body.
- The problem is in each of our bodies
there's 37 trillion cells,
and at this point now,
experiments can be run with millions of cells.
- How do you analyze
and page through all this data?
- That challenge is a really big one.
- The information needed
to create a complete cell atlas is rich,
difficult to interpret, and not easily searchable
by all of the biologists that would benefit from it.
- And so we developed a tool called 'CELLxGENE.'
- The hope with a tool like CELLxGENE
is that the time that it takes to come up with
and address hypotheses becomes very short.
- The more we have a better fundamental understanding
of how these cells work,
the better we're gonna be able to understand these diseases
and perhaps one day cure them.
The history of science teaches us
that discovery is often driven
by the development of new tools.
It's tools that enable you to ask questions
you haven't asked before.
My name's Steve Quake,
I'm the head of science at CZI.
Cell biology is at an amazing inflection point
where new technologies are revolutionizing
the kind of information one can collect about cells
and their behavior and their identities—
and we made a very large and significant investment
in developing cell atlases.
- These atlases plot out
what cells exist and where;
essentially unveiling the smallest building blocks
of the human body.
- If you wanna understand distinct features
that make the “Rockies” really unique
as compared to the plains,
the same questions can be asked of cells
that are in the liver versus the pancreas.
And so for those looking at developing drugs
or precision medicine,
having the knowledge of where diseases are acting
or where genes are acting is gonna be incredibly powerful.
- When we started making these cell atlases
it involved a small group of experts,
but as we got into it and the team grew,
we added people who had different kinds of expertise.
- Quake's team realized
that if they could improve access
and collaboration between researchers,
efforts around the world to create cell atlases
could move faster and more effectively,
and so, Chan Zuckerberg CELLxGENE was born.
- What CELLxGENE does is it makes data exploration
and analysis at scale much easier.
It's really a resource that's intended
to serve the community.
- CELLxGENE is designed to be easily navigable
and freely accessible for labs
and individuals around the world.
And so far, it's made more than 30 million cells
worth of data available
for researchers in need of single-cell data,
and for teams working on building cell atlases.
- We need to have an understanding
of what does it mean to be healthy?
What does the reference look like?
- Angela Pisco is a data scientist
at the Chan Zuckerberg Biohub,
and works on Tabula Sapiens,
a cell atlas that launched with nearly 500,000 cells
from 24 organs collected from the same 15 individuals—
and continues to grow.
- The goal of the project
is to get a comprehensive characterization
of as many tissues and organs as we can from single donors.
- Being able to look at cells captured from multiple organs
from single individuals,
removes some of the variability
and biological bias that you might see in other studies.
And so CELLxGENE has
helped the team go through and annotate
those data sets increasingly quickly.
- So we have the Tabula Sapiens samples:
We are basically cutting it to put the barcodes in
that will then let us identify which fragments
of the DNA are coming from each cell.
- In 2022, alongside three other milestone papers,
Tabula Sapiens published their benchmark first draft,
and it's already uncovered new revelations
about cells across the human body.
- When you use CELLxGENE to explore the Tabula Sapiens,
you open it up and it shows you
a plethora of different cell types
all in different clouds, different colors.
You can circle any of them and do a deep dive
into what genes they're expressing
that makes one different than the other.
- Here we can select regions
so that we can start to learn
something about what makes one region unique
and distinct from some of the middle ones.
- Working together collaboratively
across institutions enables us to make
sort of the best possible data set for people to use,
and avoid it being a Tower of Babel
where everyone's done everything a little differently
and it's not entirely compatible.
Tabula Sapiens and the other cell atlases we're working on
will have impact globally on science
because people everywhere
who are trying to understand mysteries of the cell
or their particular tissue
now have a complete
molecular portrait of those cell types;
leading us to new therapeutics
and better understanding of human disease.
- By making our data available, we really hope
to inspire the rest of the scientific community
to partner with us and really
to take a very collaborative approach
at paving the way to build the Human Cell Atlas.
- What excites me about the future of single-cell biology
and the utility of CELLxGENE
is that I think we're at the beginning,
and eventually I do believe
that it will be a foundational reference
that will be useful
for every biomedical scientist in the world.
So in the same way that we now think
of resources like the periodic table
or like the human genome,
I think that's where we're going
with single-cell biology and the Human Cell Atlas.