Study Demonstrates the Importance of Single-Cell Sequencing to
Identify Rare Cell Populations Normally Hidden in Bulk Sample Studies
BOSTON & SOUTH SAN FRANCISCO, Calif.--(BUSINESS WIRE)--
In work published in Nature this month, scientists at the Broad
Institute and Fluidigm Corporation used the C1TM
Single-Cell Auto Prep System to prepare cells for single-cell sequencing
- enabling the discovery of a subpopulation of “precocious” cells
expressing antiviral genes earlier than the majority of dendritic cells
exposed to the same antigen. Normally, the ability to detect the actions
of these “precocious expresser” cells would be lost due to averaging
across many millions of cells in bulk cell studies. With this discovery,
made possible with contributions from the Single-Cell Genomics
initiative of Fluidigm and the Broad, researchers will be able to
explore how these “precocious” cells escalate the body’s immune response
when the body is under attack.
The Nature paper also highlighted the role of cellular
heterogeneity and its importance in cell-to-cell communication during an
immune response. In typical studies, cells are studied together in one
environment, allowing the cells to communicate and signal to one
another. However, the unique properties of Fluidigm’s C1 Single-Cell
Auto PrepSystem allowed the researchers to isolate the cells
from one another to identify the specific cells expressing antiviral
genes. Because these cells were isolated, the non-expressing cells did
not surmount a response, indicating that cell-to-cell communication
plays a critical role in promoting immune response.
In addition to the discovery of a rare subpopulation of cells, this
research represented a new benchmark for sheer volume of single-cell
data. The 1,774 cells represented in this paper provide one of the
largest single-cell genomic datasets published to date and one of the
largest mRNA sequencing datasets available anywhere.
In order to identify and characterize these rare “precocious” cells,
which make up only 1% of dendritic cell populations, researchers needed
to scale up to a high number of cells. To do this, they first needed to
solve two key problems: how to prepare single-cell libraries for
thousands of cells, and how to sequence such large sample numbers
To prepare the huge number of single-cell libraries, the researchers
relied on the C1 Single-Cell Auto Prep System, which had just
been introduced to the marketplace at the time these experiments began.
The C1 system’s microfluidic technology enabled the
researchers to rapidly and reliably isolate, process, and profile
individual cells for genomic analysis. During the study, the group
discovered that they could achieve stable data with single cells at less
than one million reads (compared to run rates of at least 5 to 10
million reads when conducting bulk mRNA sequencing). The ability to
obtain reliable data faster greatly reduced the cost of running the
For access to the complete paper -- Single-cell RNA-seq reveals dynamic
paracrine control of cellular variation, Nature. 2014 Jun
19;509(7505):363-9 -- please visit: to http://info.fluidigm.com/Shalek_Et_Al.html.
Single-Cell Genomics initiative
In 2012, the Broad Institute’s Genomics Platform and Fluidigm
Corporation (NASDAQ:FLDM) established the Single-Cell Genomics
initiative dedicated to accelerating the development of research methods
and discoveries in mammalian single-cell genomics. The Single-Cell
Genomics initiative also acts as a hub for collaboration among
single-cell genomics researchers in many pioneering fields, including
stem cells and cancer biology. The initiative is housed at the Broad
Institute in Cambridge, Massachusetts, and features a complete suite of
Fluidigm single-cell tools, protocols and technologies, most notably the
C1 Single-Cell Auto Prep System and the BioMark™ HD System.
Single-Cell Auto Prep System is based on the company’s innovative
microfluidic technology that enables researchers to rapidly and reliably
isolate, process, and profile individual cells for genomic analysis.
Scientists can extract, reverse transcribe, amplify, and ultimately
detect and analyze cell activity using one technology thereby reducing
the variability caused by multi-platform technical errors.
In the experiments that supported this newly announced research, up to
five C1 systems were incorporated to work with a total cell
count of 1,774 individual cells producing successful single-cell
libraries from biologically meaningful experiments.
This paper is the 10th peer-reviewed publication featuring
the C1 system.
Fluidigm (NASDAQ:FLDM) develops, manufactures, and markets life science
analytical and preparatory systems for growth markets such as
single-cell biology and production genomics. We sell to leading academic
institutions, clinical laboratories, and pharmaceutical, biotechnology,
and agricultural biotechnology companies worldwide. Our systems are
based on proprietary microfluidics and multi-parameter mass cytometry
technology, and are designed to significantly simplify experimental
workflow, increase throughput, and reduce costs, while providing
excellent data quality. Fluidigm products are provided for Research Use
Only. Not for use in diagnostic procedures.
For more information, please visit: http://www.fluidigm.com.
Fluidigm, the Fluidigm logo, C1, andBioMark are
trademarks or registered trademarks of Fluidigm Corporation.
About the Broad Institute of MIT and Harvard
The Eli and Edythe L. Broad Institute of MIT and Harvard was launched in
2004 to empower this generation of creative scientists to transform
medicine. The Broad Institute seeks to describe all the molecular
components of life and their connections; discover the molecular basis
of major human diseases; develop effective new approaches to diagnostics
and therapeutics; and disseminate discoveries, tools, methods, and data
openly to the entire scientific community.
Founded by MIT, Harvard, and its affiliated hospitals, and the visionary
Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute
includes faculty, professional staff and students from throughout the
MIT and Harvard biomedical research communities and beyond, with
collaborations spanning over a hundred private and public institutions
in more than 40 countries worldwide. For further information about the
Broad Institute, go to http://www.broadinstitute.org.
Howard High, 650-266-6081 (office)
Fellow, Corporate Communication and Press Relations
Haley Bridger, 617-714-7968
Manager of Science
Communications and Media Relations
Source: Fluidigm Corporation