GSM6416007: B6_5m_cereb_tsection_inputforChIPseq_rep1; Mus musculus; ChIP-Seq
Cultured cells were permeabilized with PBS +0.25% Triton X-100 and stained for Lamin B1, and then a secondary HRP antibody. THe TSA reaction was performed according the kit [Biotin-XX-Tyramide Superboost kit (Invitrogen, #2005939)]. The cells were digested with Proteinase K in RIPA buffer overnight. DNA was extracted using phenol/chloroform/isoamy alcohol. Pure DNA was sonicated with a Misonix sonicator and biotinylation of DNA was monitored by dot blot onto positively charged nylon membranes. Streptavidin pulldown was done in a manner similar Chen, et al., 2018 and we used the modified protocol for washes. For tissue sections, cells/nuclei were isolated by brief sonication and collagenase type 2 digestion. The TSA reaction was done as described for cultured cells. Chromatin fragmentationn was done using a combination of sonication and MNase digestion in RIPA buffer and Streptavidin pulldown was done for 1 hour at room temperature. Rubicon Genomics (Takara) ThruPlex 48 kit.