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Chunk #24 — Methods — H3K9Ac ChIP-Seq

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A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research.
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We identified the Millipore anti-H3K9Ac mAb (catalog # 06-942, lot: 31636) as a robust monoclonal antibody for our chromatin immunoprecipitation experiment. 50 milligrams of gray matter was dissected on ice from biopsies of the DLPFC of each ROS and MAP subject. The tissue was minced in a wash of ice cold PBS containing the Complete Protease Inhibitor Cocktail (Roche 11 836 170 001) and cross-linked with 1% formaldehyde at room temperature for 15 mins and quenched with 0.125M Glycine. The tissue was then homogenized in cell lysis buffer (20 mM Tris-HCl pH8.0, 85 mM KCl, 0.5% NP 40) using the Tissue Lyser and a 5mm stainless steel bead. Then the nuclei were lysed in nucleus lysis buffer (10 mM Tris-HCl, pH7.5, 1% NP 40, 0.5% sodium deoxycholate, 0.1% SDS) and chromatin was sheared using a Branson Sonifier 250 set to 40% amplitude for 0.7 s on and 1.3 s off for 6 minutes with the thermal block set at −6 ˚C to generate the optimal majority fragment size range between 200 and 600 bp. Samples were then centrifuged to pellet