Resources

Useful links:

CyTOF & CODEX Mini-course

Software:

Citrus:

  • Description: Citrus is an algorithm that clusters cells from multiple samples (patients, stimulations, etc) into a hierarchical tree and then identifies the cell types from all levels of hierarchy that are significantly associated with the sample grouping, disease outcome, or response to specific stimulations.
  • Article:
  • User manual and downloads: https://github.com/nolanlab/citrus

SPADE:

VorteX:

CYT:

DREMI:

CyTOF Core:

Bead Normalization:

  • Description: Software for bead normalization, which is a method for correcting both short- and long-term signal fluctuations in mass cytometry data by measuring metal-embedded polystyrene beads along with cell samples. It is distributed both as MATLAB code and as a standalone application (MATLAB not required).
  • Article:
  • User manual and downloads: https://github.com/nolanlab/bead-normalization/releases/latest

Single Cell Debarcoding:

  • Description: The Single Cell Debarcoder is a tool for the deconvolution of a barcoded FCS file into separate FCS files of each barcode population. It is distributed both as MATLAB code and as a standalone application (MATLAB not required).
  • Article:
    • Palladium-based Mass-Tag Cell Barcoding with a Doublet-Filtering Scheme and Single Cell Deconvolution Algorithm.
    • Eli R. Zunder, Rachel Finck, Gregory K. Behbehani, El-ad D. Amir, Smita Krishnaswamy, Veronica D. Gonzalez, Cynthia G. Lorang, Zach Bjornson, Matthew H. Spitzer, Bernd Bodenmiller, Wendy J. Fantl, Dana Pe�er, Garry P. Nolan.
    • Nature Protocols, 2015 http://www.nature.com/nprot/journal/v10/n2/abs/nprot.2015.020.html
  • User manual and downloads: https://github.com/nolanlab/single-cell-debarcoder/releases/latest

Key experimental methods

Flow:

CyTOF:

Viability Staining:

  • Description: 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.
  • Article:
    • A platinum-based covalent viability reagent for single cell mass cytometry.
    • Fienberg H, Simonds EF, Fantl WJ, Nolan GP, Bodenmiller B.
    • Cytometry A, 2012 http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22067/abstract
  • Cytobank report: http://reports.cytobank.org/103/v1

Isotope Barcoding:

  • Description: 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.
  • Article:
    • 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 http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22573/abstract
  • Cytobank public dataset: https://www.cytobank.org/cytobank/experiments?project=627
  • Article:
    • Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.
    • Bernd Bodenmiller, Eli R. Zunder, Rachel Finck, Tiffany J. Chen, Erica S. Savig, Robert V. Bruggner, Erin F. Simonds, Sean C. Bendall, Karen Sachs, Peter O. Krutzik, Garry P. Nolan.
    • Nature Biotechnology, 2012
  • Cytobank Report : http://reports.cytobank.org/105/v2

Clinical Correlate Informatics:

  • Description: 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.
  • Article:
    • 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.
      http://stm.sciencemag.org/content/6/255/255ra131
  • Cytobank public dataset: https://www.cytobank.org/cytobank/experiments?project=609

Data Normalization and Standarization with beads:

  • Description: 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.
  • Article:
  • Cytobank Report: http://reports.cytobank.org/111

Single Cell Debarcoding:

 




Professor Garry Nolan

Professor, Microbiology & Immunology - Baxter Laboratory

Member, Bio-X Member, Child Health Research Institute Member, Stanford Cancer Institute

Full bio

Quick Contact

Primary Contacts:
For procedural questions regarding MTAs, Phoenix cells, or directions to the lab, please contact Shama Choudhry.
Executive Assistant:
Shama Choudhry
Tel: (650) 725-7002
Fax: (650) 723-2383

shamac@stanford.edu