GSE106346
Neural induction by the node and placode induction by head mesoderm share an initial state resembling neural plate border
Purpose:  The goal of this study is to identify similarities and differences in the induction of the central nervous system and the sensory placodes in chick. Method: mRNA profiles for central and anterior pre-steak epiblast, neural plate, anterior and posterior pre-placodal region, non-neural epiblast, gastrula stage area opaca exposed to Hensen''s node for 5 hours and control area of opaca from the same stage.  Deep sequencing was carried with Illumina HiSeq 2000. After filtering low quality reads, alignment was carried using TopHat2, differential expression analysis was done using R-package (easyRNA-seq and DSEq). Results:  Despite the differences in inducing tissues (i.e. node and lateral head mesoderm) and in the final outcome (neural plate and pre-placodal region), the initial set of genes induced by both tissues is largely identical. We define this transcriptional signature as ''pre-neural state'', and demonstrate its functional significance for both inductive processes.  An unbiased approach using GENEI3 and community clustering reveals  the gene regulatory modules characterising the transcirptional states of pre-neural, neural and placodal cells. Conclusion:  Induction of the neural plate and the pre-placodal region initially share common features, and diverge later.  The pre-neural state is similar to the neural plate border and pre-streak epiblast state. Overall design: Overall design:  mRNA profiles for 8 biological samples representing different stages in neural and pre-placodal induction were processed for deep sequencing data by Illumina HiSeq 2000.