URD

URD is an R package designed for reconstructing transcriptional trajectories underlying specification or differentiation processes in the form of a branching tree, using single cell RNA-sequencing data. It is named after the Norse mythological figure who nurtures the world tree and decides all fates.

 

URD is described and applied to early zebrafish embryogenesis in:

Farrell JA*, Wang Y*, Riesenfeld SJ, Shekhar K, Regev A*, Schier AF*. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 26 Apr 2018. doi: 10.1126/science.aar3131

Browsing the Data

The zebrafish embryogenesis data (38,731 cells, 12 developmental time points from 3.3–12 hours post fertilization) can be browsed in two forms:
 

  1. Easiest/Quickest: Browse the data in the Broad Single-cell Portal (https://portals.broadinstitute.org/single_cell/study/single-cell-reconstruction-of-developmental-trajectories-during-zebrafish-embryogenesis). This allows plotting the expression of genes of interest on the 3D force-directed layout, tSNE projection, or spatially assigned 50% epiboly cells.
     
  2. Best: Download and install URD (see "Getting URD" below), then download the zebrafish data as a pre-processed URD object (requires logging into the Broad Single-cell Portal). This allows more responsive plotting on the 3D force-directed layout, the dendrogram layout, or the tSNE projections (including dual-color plotting of multiple genes), as well as isolation of particular cell populations, differential expression, and more.



Getting URD

URD is an R package hosted in Github (https://github.com/farrellja/URD). Detailed installation instructions are located in the repository.
 

Getting the data

If you want to do your own analysis with our data, you can obtain it in two forms:

  1. The processed counts matrix can be downloaded and used as a starting point for your own analysis:  (https://portals.broadinstitute.org/single_cell/data/private/single-cell-reconstruction-of-developmental-trajectories-during-zebrafish-embryogenesis?filename=URD_Dropseq_Expression_Log2TPM.txt.gz — requires logging into the Broad Single-cell Portal).
     
  2. BAM files are deposited in NCBI GEO under accession number GSE106587.



Contact Us

For questions regarding URD, please email Jeff Farrell (jfarrell@g.harvard.edu), Yiqun Wang (yiqunwang@g.harvard.edu), or Alexander Schier (schier@fas.harvard.edu).