Traditionally, lineage markers are used to identify changes in phenotypic states. While these markers can be good indicators of differentiation potential, there are two major limitations with this approach. First, there are multiple genes that are associated with each lineage so simply looking at one can often be misleading. Second, this approach only works for classifying states with well-characterized marker genes but would not work for a comprehensive characterization of the function in the cell. Therefore, we decided to take a different approach and look at the entire gene expression profile of each lincRNA knockdown to determine what cell state each lincRNA resembles.
