title: GSM5914822: Adnp_SETDBsh1_UT_R1; Mus musculus; ChIP-Seq
library_construction_protocol: genomic DNA ChIP-seq was carried out as previously described (Balestrieri et al. 2018). Briefly, 106 lentiviral-infected BMDM cells (H3K27ac, H3K9me3, PU.1) or 20 x 106 lentiviral-infected BMDM cells (CTCF) were fixed with 1% of formaldehyde (Merck cod. 252549) for 10 min at RT and lysed to prepare nuclear extracts.   40 x 106 lentiviral-infected BMDM cells (2% of formaldehyde fixation) were used for Adnp ChIP-seq. After chromatin shearing by sonication with a Branson Ultrasonics™ Sonifier™, lysates were incubated overnight at 4°C with protein G Dynabeads (Invitrogen, cod.10009D) previously coupled with 1 μg of anti-histone antibody or 10 μg of anti-TF antibody (all the antibodies are listed in the Suppl. Table 9). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Immunoprecipitated chromatin was eluted and cross-link reverted overnight at 65°C. DNA was purified with QIAquick PCR Purification Kit (QIAGEN) and then quantified with QuantiFluor (Promega). DNA libraries were prepared for NextSeq500 sequencing as described (Austenaa et al. 2021). The purified DNA libraries were quantified with the Quantifluor reagent (Cod.E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the High Sensitivity Assay HD5000 (Agilent cod.5067-5592). Library DNA were diluted to a working concentration of 4 nM and Single Reads (76bp) sequenced on an Illumina NextSeq500 platform.