Single-cell RNA-Seq

We have released the first round of data from our single-cell RNA-Seq experiments. You can explore the data in our web application SCeNGEA at The data are also available for download as an R object (in the monocle cellDataSet format) on the download page.

We are performing 10x single-cell RNA-Seq on FACS-isolated neurons. Using 52,412 sequenced cells, 109/118 neuronal classes have been identified and computationally assigned to a cluster based on their gene expression fingerprint (93 confidently, 16 tentatively), and 9/118 classes have not been annotated yet. Completed experiments:

  • rab-3 (pan-neural):   8,625 cells
  • unc-47 (pan-GABA 1):  1,176 cells
  • unc-47 (pan-GABA 2):  2,933 cells
  • nmr-1:  2,250 cells
  • eat-4 (pan-glutamate):  6,136 cells
  • ift-20 (pan sensory neurons):  3,935 cells
  • unc-3:  4,481 cells
  • cho-1 (pan-cholinergic 1): 3,474 cells
  • cho-1 (pan-cholinergic 2): 3,107 cells
  • tph-1; ceh-10: 3,331 cells
  • acr-2 (cholinergic MN): 10,299 cells
  • ceh-34 (pan-pharyngeal): 2,305 cells

Pending experiments:

  • unc-86: targeting 5,000 cells

We are currently validating the neuronal classes identified by creating novel expression markers.