Capture-C in somite-matched pre-somitic mesoderm from Smchd1GFP/GFP, Smchd1MD43-GFP/MD43-GFP, Smchd1+/+ and Smchd1MD43/MD43 embryos.

Capture-C from in situ HiC libraries in tailbud tissue containing pre-somitic mesoderm (PSM) dissected from Smchd1GFP/GFP, Smchd1MD43-GFP/MD43-GFP, Smchd1+/+ and Smchd1MD43/MD43 embryos E8.5 embryos at the 7-9 somite stage of development. Somite stage is a good indicator of the precise stage of embryonic development. Embryonic somite-matched PSM tissue was dissected, dissociated and crosslinked to make DpnII-digested in situ HiC libraries, then captured using a custom protocol for low input. Each library was made from a pool of tissue 2 embryos of the same genotype. RNA capture oligos were designed and ordered from Agilent SureSelect, to enrich for reads representing contacts within the four Hox clusters, of central interest to this publication, and other known Smchd1 target loci (clustered protocadherins and various olfactory receptor gene clusters).