Multiplex cis-regulatory analysis.

Recent progress in multiplex cis-regulatory analysis has increased the speed of identifying enhancers and promoters, and enabled efficient incorporation of cis-regulatory information into gene regulatory network models. Three types of barcode reporters have been developed for multiplex reporter assays in sea urchin embryos: 13-tags and 129-tags for QPCR, 130 Nanotags for NanoString, and 100 million N25-tags for next-generation sequencing. In this chapter, to facilitate adoption of high-throughput cis-regulatory analysis in sea urchin embryos, I provide practical guidelines to best utilize barcode reporters that are compatible with either QPCR or next-generation sequencing. I expect that the guidelines are also applicable to other invertebrate embryos.