Chromatin preparation for ChIP-seq in Oikopleura dioica

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.
Here we describe an optimized protocol for collection, fixation, lysis and chromatin sonication of three developmental stages of the chordate model Oikopleura dioica, an emergent model organism for chordate developmental and evolutionary biology studies.

Includes troubleshooting section of commonly encountered problems.