GSM3884601: DPY27_HiChIP_hermaphrodites_rep2; Caenorhabditis elegans; OTHER
Embryos were crosslinked with 1.1% formaldehyde. Nuclei were isolate in a dounce and recrosslinked with 1% formaldehyde for 10 minutes.Chromatin was digested by DpnII, filled in with biotin-dCTP, and ligated. DNA was then isolated for Hi-C library prep. For HiChIP, ligated chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-DPY27 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation. Libraries were constructed using the standard protocol or using a Tn5 library prepartion protocol. Genomic fragments were end repaired, A-tailed by adding  adenosine to  the 3' ends of fragment using Klenow fragment (3' to 5' exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). For Tn5 protocol, samples were incubated with Tn5 transposase in the presence of adaptors. Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.
GEO Accession
GSM3884601