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Cell homogenates were sonicated and boiled in LDS sample buffer (Invitrogen) in the presence of 25 mM DTT.
Protein samples were boiled for 5 min in Novex NuPage sample buffer (Invitrogen) in the presence of 2.5% β-mercapthoethanol and separated through Bis-Tris 4 12% polyacrylamide gradient NuPage gels using the Novex XCell Sure Lock electrophoresis cell (Invitrogen).
Protein samples (recombinant Otolin and ground-up P0 mouse inner ear) were suspended in NuPAGE LDS sample buffer (Invitrogen) in the presence or absence of reducing agent (β-mercaptoethanol), heated at 90°C for 10 min, and separated on 4 12% NuPAGE Bis-Tris gels in NuPAGE MOPS SDS running buffer at 195 volts for 4 hr.
ProBond™ resin (50 μl; Invitrogen) precharged with Ni2+ was added to 1.2 ml of native purification buffer (Invitrogen) in the presence or absence of 0.8 pmol of bvCTCF (baculovirus recombinant Ctcf) recombinant His-tagged protein [ 18].
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Protein was then transferred to a Hybond-LFP Polyvinylidene difluoride (PVDF) membrane (GE Healthcare, Buckinghamshire, UK) at 200 mA for 90 min at 4°C using the NuPAGE transfer buffer (Invitrogen) in a Criterion Blotter (BioRad, Hercules, CA).
Gels were blotted onto nitrocellulose membranes (Invitrogen), immersed in NuPage LDS transfer buffer (Invitrogen) in a cold room (4°C) overnight applying 30 V.
A 4 μl aliquot of this reverse transcription solution was used for PCR using 50 pmol of each specific primer, 10 mmol dNTP (Invitrogen), 1.5 mmol/l MgCl2 (Invitrogen), and 10 × PCR buffer (Invitrogen) in a total volume of 50 μl (see Table 2 for PCR amplification conditions).
Gels were run for 60 min at 180 V in 1× NUPAGE MES SDS running buffer (Invitrogen #NP0002) in the presence of NuPAGE antioxidant (Invitrogen #NP0005).
The cDNA was fragmented at 37°C for 10 minutes in a reaction mixture consisting of purified cDNA and DNase I (Roche Applied Science, Indianapolis) in One-Phor-All buffer (Invitrogen, Carlsbad, CA) in the order of 0.06 U DNase/μl of cDNA.
Ten μg of protein extract was loaded and separated using MOPS running buffer (Invitrogen, UK), in accordance with the manufacturer's instructions.
Ds cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN).
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