Illumina sequencing of mixed age embryos was carried out, resulting in embryonic transcriptomes consisting of 40605 contigs for C.echinata (N50 = 1080 bp) and 48536 contigs for F.lizardensis (N50 = 1496 bp). 
Illumina sequencing
The transcriptomes have been annotated against Swiss-Prot and were sufficiently complete to enable the identification of orthologs of many key genes controlling development in bilaterians. 
Swiss-Prot
In situ hybridization was used to examine the expression of the developmentally important genes brachyury, chordin and forkhead. 
in situ hybridization