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Cells were washed with ice-cold phosphate-buffered saline (PBS) and resuspended in RSB buffer (10 m M Tris (pH 7.4); 10 m M NaCl; 1.5 m M MgCl2; 10 m M NaF; supplemented with 0.15 m M PMSF; 1 m M DTT; 0.2 m M Na3VO4) and incubated 10 min on ice for swelling.
To extract nuclei for DNMT3a-like immunolabeling, cortical tissue was homogenized in 2mL 1× RSB buffer (100 mM NaCl, 30mM MgCl2, 100 mM Tris-HCl, pH 7.5) with 1% NP-40, mixed with 8 mL 1× RSB, and centrifuged in a swing-bucket rotor at 1000×g for 10 min at 4°C.
Adaptor-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics) and eluted in 22.5 µl resuspension buffer (RSB) buffer.
For acid extraction of histones cells were washed in RSB buffer (10 mM HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2), then lysed in RSB plus 0.5% NP-40 for 10 min on ice.
The supernatant was discarded and the pellet was resuspended in a hypotonic RSB buffer (10 mM NaCl, 2.5 mM MgCl2, 10 mM Tris base, pH 7.5) and allowed to swell.
Cells were lysed in 20 ml 1× reticulocyte standard buffer (RSB) buffer (10 mM Tris pH7·4, 10 mM NaCl, 3 mM MgCl2) with 0·1% NP-40 for 7 10 min and the nuclei pelleted.
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The beads were washed three times with RSB-100 buffer.
The treatment of the RSB-magik buffer further removed the cytoskeleton, leaving behind the nuclei and their attached filaments.
The beads were washed three times with RSB-100 buffer (10 mM Tris-HCl [pH 7.4], 100 mM NaCl, 2.5 mM MgCl2, 0.4% Triton X-100) and resuspended in 150 μl RSB-100 with 40 U RNase-OUT (Invitrogen) and 5 μg of glycogen.
The remaining pellets, containing DNA as well as proteins tightly associated with DNA, were washed in reticulocyte buffered buffer (RSB: 10 mM NaCl, 10 mM Tris-HCl pH 7.5 and 1.5 mM MgCl2) and finally resuspended in RSB and HCl 0.4N to obtain HCl-soluble proteins (Castiglia et al., Neurochem Res (1994); Cestelli et al., Cell Mol Neurobiol.
Then, they were resuspended in 1 ml ice-cold Hypotonic Buffer (RSB: 10 mM HEPES-KOH, 10 mM KCl, 1.5 mM, MgCl2, pH 7.5) containing complete Protease Inhibitor Cocktail (EDTA), 1 mM activated Na3VO4, 10 mM NaF, 10 μM MG132 and 5 mM N-ethylmaleimide and incubated for 10 min. Cells were ruptured using an ice-cold dounce homogenizer (approximately 40 strokes).
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CEO of Professional Science Editing for Scientists @ prosciediting.com