Resources for CyTOF and Single-Cell Analysis
Curated resources, training materials, and key experimental methods for mass cytometry and single-cell analysis.
Useful Links
- CyTOF Mass Cytometer — A one-of-a-kind mass cytometer that allows precise quantification of dozens of markers on single cells.
- Cytobank — An online repository for single-cell data that offers a wealth of analytical and visualization tools.
- Smart Tube System — A compact, fully automated system for blood sample collection, storage and processing.
CyTOF/CODEX Training Courses
The Nolan Lab has offered hands-on mini-courses in mass cytometry and CODEX multiplexed imaging:
- CyTOF/CODEX Mini-Course 2018
- CyTOF/CODEX Mini-Course 2014
- CyTOF/CODEX Mini-Course 2013
- CyTOF/CODEX Mini-Course 2012
Key Experimental Methods
Protocols and publications for core mass cytometry techniques developed at the Nolan Lab.
CyTOF Viability Staining
A mass cytometry-specific methodology for live/dead staining, which uses the platinum-containing chemotherapy drug cisplatin. In a 1-min incubation step, cisplatin preferentially permeates nonviable cells from both adherent and suspension cultures and binds to the DNA, resulting in a platinum signal that is detectable on CyTOF.
A platinum-based covalent viability reagent for single cell mass cytometry. Fienberg H, Simonds EF, Fantl WJ, Nolan GP, Bodenmiller B. Cytometry A, 2012
Isotope Barcoding
Barcoding cells from different samples with specific isotope combinations allows mixing, staining and measuring multiple samples together in one go, thus eliminating multiple sources of sample-to-sample variability.
Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining. Gregory K. Behbehani, Colin Thom, Eli R. Zunder, Rachel Finck, Brice Gaudilliere, Gabriela K. Fragiadakis, Wendy J. Fantl, Garry P. Nolan. Cytometry A, 2014
Clinical Correlate Informatics
The speed and ease of recovery after surgery differ for every patient, and determining the mechanisms that drive recovery could lead to patient-specific recovery protocols. Mass cytometry was used to characterize postsurgical immunological insult at a single-cell level and to identify a surgical immune signature that correlates with clinical recovery across patients. Specifically, cell signaling responses, but not cell frequency, were linked to recovery. Moreover, the correlated signaling responses occurred most notably in CD14+ monocytes, suggesting that these cells may play a predominant role in surgical recovery. The consistency of this signature across patients suggests a tightly regulated immune response to surgical trauma, which may form the basis of a diagnostic guideline for personalized postsurgical care.
Clinical recovery from surgery correlates with single-cell immune signatures Brice Gaudillière, Gabriela K. Fragiadakis, Robert V. Bruggner, Monica Nicolau, Rachel Finck, Martha Tingle, Julian Silva, Edward A. Ganio, Christine G. Yeh, William J. Maloney, James I. Huddleston, Stuart B. Goodman, Mark M. Davis, Sean C. Bendall, Wendy J. Fantl, Martin S. Angst, Garry P. Nolan. Science Translational Medicine, 2014.
Data Normalization and Standardization
A method to correct both short- and long-term signal fluctuations in mass cytometry data by measuring metal-embedded polystyrene beads along with cell samples.
Normalization of Mass Cytometry Data with Bead Standards. Rachel Finck, Erin F. Simonds, Astraea Jager, Smita Krishnaswamy, Karen Sachs, Wendy Fantl, Dana Pe’er, Garry P. Nolan, Sean C. Bendall. Cytometry A, 2013