Chromatin preparation for ChIP-seq in Oikopleura dioica

<p>Chromatin immunoprecipitation (ChIP) is a widely used molecular technique for binding site identification of DNA-associated proteins in many organisms. Although well established, its use in non-model organisms usually requires extensive protocol optimisation.<br>Here we describe an optimized protocol for collection, fixation, lysis and chromatin sonication of three developmental stages of the chordate model <em>Oikopleura dioica</em>, an emergent model organism for chordate developmental and evolutionary biology studies.</p> <p>Includes troubleshooting section of commonly encountered problems.</p>