Mechanical tensions regulate gene expression in the Xenopus laevis neuroectoderm

During gastrulation and neurulation, chordamesoderm and overlying neuroectoderm of vertebrate embryo are converged under the control of specific genetic program to the dorsal midline, simultaneously extending along it. To reveal genes regulated by mechanical tensions developed as a result of these morphogenetic movements we compared transcriptomes of artificially stretched neuroectodermal explants of Xenopus laevis midgastrula embryos with the non-stretched one. Total RNA was extracted from cell lysed with Trisol reagent and PureLink RNA Micro Kit according to manufacture instruction. Quality was checked with BioAnalyser and RNA 6000 Nano Kit. PolyA RNA was purified with Dynabeads mRNA Purification Kit. Illumina library was made from polyA RNA with NEBNextNEBNext RNA Library Prep Kit for Illumina according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample. Reads mapping was done using tophat2 software v.2.0.9. As a reference genome we used Xenopus Laevis build 6 (http://www.xenbase.org/genomes/static/laevis.jsp). For quantification, we used cufflinks v2.1.1.