RT Journal
A1 Barsi, Julius C.
A1 Tu, Qiang
A1 Davidson, Eric H.
T1 General approach for in vivo recovery of cell type-specific effector gene sets
JF Genome Research 
JO Genome Research 
YR 2014 
FD May 01 
VO 24 
IS 5 
SP 860 
OP 868 
DO 10.1101/gr.167668.113 
UL http://genome.cshlp.org/content/24/5/860.abstract 
AB Differentially expressed, cell type-specific effector gene sets hold the key to multiple important problems in biology, from theoretical aspects of developmental gene regulatory networks (GRNs) to various practical applications. Although individual cell types of interest have been recovered by various methods and analyzed, systematic recovery of multiple cell type-specific gene sets from whole developing organisms has remained problematic. Here we describe a general methodology using the sea urchin embryo, a material of choice because of the large-scale GRNs already solved for this model system. This method utilizes the regulatory states expressed by given cells of the embryo to define cell type and includes a fluorescence activated cell sorting (FACS) procedure that results in no perturbation of transcript representation. We have extensively validated the method by spatial and qualitative analyses of the transcriptome expressed in isolated embryonic skeletogenic cells and as a consequence, generated a prototypical cell type-specific transcriptome database.