Scientific Research Services for JAX Faculty
Single Cell Biology Laboratory
The Single Cell Biology Laboratory (SCBL) develops and offers single cell capabilities to JAX faculty and, through a Single Cell Genomics Center agreement, University of Connecticut faculty. The primary lab is located at JAX-GM in Farmington, Connecticut with a satellite lab in JAX-MG, Bar Harbor, Maine. The SCBL is directed by Paul Robson and is currently staffed with 7 scientists.
We employ a suite of single cell transcriptomics technologies. This includes droplet-based 3’-end counting methods, microfluidic chip and plate-based full-length RNA-seq approaches, as well as individual sample-based approaches, for instance, downstream of laser capture micro-dissection. We have extensive experience in all aspects of single cell transcriptomics and continue to generate large amounts of data (see Figure) from a wide variety of mouse and human normal and diseased tissues.
In addition to these established capabilities, the team spends significant time developing new technologies in the single cell space. We currently are developing circulating tumor cell enrichment, characterization, and model generation strategies. We are also implementing imaging mass cytometry approaches to provide some spatial context to cell-types within tissues. We have also developed methods to enable biologists to interact and mine single cell transcriptome data, specifically the CellView app developed by Mohan Bolisetty within the group.
CellView: Interactive exploration of high dimensional single cell RNA-seq data
CellView is a web application that allows easy and intuitive exploration of gene expression to validate clustering, describe heterogeneity, and identify and discover new cell types in complex single cell transcriptome data sets. Data we generate and initially cluster is delivered to our end users as an R dataset (.Rds) file with three pre-computed data frames holding gene expression, clustering information and gene symbol maps. These data sets can then be uploaded to the CellView app for visualization, exploration, and interactive analysis. Links to CellView app can be found here:
The image below is a rendering of an 80,000 single cell transcriptome project generated in collaboration with Bill Skarnes. This represents data from undifferentiated human iPS cells and a 6 day time course of these cells differentiated down 4 lineages (mesoderm, endoderm, ectoderm, and extra-embryonic).