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Gels were blotted onto nitrocellulose membranes (Invitrogen), immersed in NuPage LDS transfer buffer (Invitrogen) in a cold room (4°C) overnight applying 30 V.
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).
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).
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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].
Proteins were transferred overnight at 4°C in 'NuPAGE Transfer Buffer' (Invitrogen) to a PVDF membrane (Amersham Pharmacia, PA), blocked with 'SuperBlock' buffer (Pierce, IL) for 1 hour, and probed with respective antibodies as above.
Adr1 DBD was eluted by boiling in 4× LDS loading buffer (Invitrogen), run on a 12% gel (Invitrogen) with protein standards, and visualized with a Storm Phosphorimager.
The extraction was quantified, diluted in 1 × NuPAGE/LDS loading buffer (Invitrogen), heated in 95 °C dry heater (Labnet, Woodbridge, NJ, USA) for 5 min, and loaded in 10% NuPAGE/Bis/Tris gel (Invitrogen) with NuPAGE/MES/SDS buffer (Invitrogen).
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).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com