GSM7845263: RAW 264.7_LPS; Mus musculus; ChIP-Seq
MED1 ChIP-seq was carried out as previously described (Gualdrini et al., 2022). Briefly, cells were were scraped in PBS, incubated for 45 min with 2 mM DSG in PBS, washed twice, and then incubated with 1% formaldehyde in PBS for 10 min followed by quenching with 125 mM glycine and lysed to prepare nuclear extracts. After chromatin shearing by sonication with a Branson Ultrasonics Sonifier, lysates were incubated overnight at 4°C with protein G Dynabeads (cat. no.10009D, Invitrogen) previously coupled with tetra-acetylated histone H4 (cat. no. 06866, Millipore)  MED1 antibody (cat.no. A300-793A, Bethyl). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM HEPES-KOH at pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycho- late). Immunoprecipitated chromatin was eluted and cross-link-reverted overnight at 65°C. DNA was purified with QIAquick PCR purification kit (cat. no. 28106, Qiagen) and then quantified with QuantiFluor (cat. no. E2670, Promega). DNA libraries were prepared as previously described (Austenaa et al., 2021). The purified DNA libraries were quantified with the Quantifluor reagent (cat. no. E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the high-sensitivity assay HD5000 (cat. no. 5067-5592, Agilent). DNA libraries were diluted to a working concentration of 4 nM and 50-bp single reads sequenced on an Illumina Novaseq6000 platform.