The approaches used to generate data for this project involve:

  • Multigene correlation analysis across finely distinguished developmental stages in vivo
  • Experimental manipulation of early T-cell development in vitro
  • Perturbation analysis by gain and loss of transcription factor function at particular stages, correlated with effects on development and gene expression
  • Perturbation analysis by addition or removal of Notch ligands from environment
  • Genome-wide prediction of transcription factor-target linkages
  • Chromatin immune precipitation and genome-wide analysis to assess active cis-regulatory sites


Sources of material:

sourcesWe use adult or fetal mouse hematopoietic stem cells or defined immature cell types from the thymus and grow them in culture dishes to control the developmental environment of HSCs.  These cells can develop into T cells if and only if the environment expresses Notch ligands.

We use a variety of experimental technologies to study T cell development.


Using Fluorescence Assisted Cell Sorting (FACS), we can track the development of individual cells.

FACS analysis has led us to extremely fine-scale resolution of stages, subdividing the conventional DN1 – 4 stages for precise temporal correlations.

Using Quantitative mRNA measurements, we have been able to establish the order in which some key events must occur for T cell development.



Some of the computational tools we are currently using within this project are: