Assessment of engineered cells using CellNet and RNA-seq

Nat Protoc. 2017 May;12(5):1089-1102. doi: 10.1038/nprot.2017.022. Epub 2017 Apr 27.


CellNet is a computational platform designed to assess cell populations engineered by either directed differentiation of pluripotent stem cells (PSCs) or direct conversion, and to suggest specific hypotheses to improve cell fate engineering protocols. CellNet takes as input gene expression data and compares them with large data sets of normal expression profiles compiled from public sources, in regard to the extent to which cell- and tissue-specific gene regulatory networks are established. CellNet was originally designed to work with human or mouse microarray expression data for 21 cell or tissue (C/T) types. Here we describe how to apply CellNet to RNA-seq data and how to build a completely new CellNet platform applicable to, for example, other species or additional cell and tissue types. Once the raw data have been preprocessed, running CellNet takes only several minutes, whereas the time required to create a completely new CellNet is several hours.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cell Differentiation*
  • Computational Biology / methods*
  • Cytological Techniques / methods*
  • Gene Expression Profiling*
  • Genotyping Techniques / methods*
  • Mice
  • Pluripotent Stem Cells / physiology*
  • Sequence Analysis, RNA*