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7 protocols using ab21635

1

Quantifying DRG Neuron Protein Levels

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Lysates from DRG neurons were run on 4-12% Bis-Tris gradient gels and proteins were transferred to PVDF membranes that were incubated with antibodies to REST (Abcam ab21635, 1:1000), using anti-β-actin as a loading control. Quantitation of western blot results was carried out with ImageJ software.
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2

Western Blot Analysis of NSC Proteins

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Protein lysate (Shanghai Beyotime Biotechnology Co., Shanghai, China) was added to the NSCs and frozen brain tissues to extract total protein. The Bradford method (Thermo Fisher Scientific Inc., Waltham, MA, USA) was used to assess protein quality. Total protein (50 μg) was then used for 12% SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) electrophoresis and transferred onto PVDF membranes (Millipore, Billerica, MA, USA). After blocking with 5% skim milk at 37°C for 1 hr, the membranes were incubated with rabbit anti-mouse NRSF (ab21635,1: 500), MOR (ab1009,1: 700), DOR (ab83775, 1: 1,000), Bcl-2 (ab32124,1: 1,000), Bax (ab32053, 1: 1,000), and β-actin (ab8227, 1: 1,000) monoclonal antibodies (Abcam, Inc., Cambridge, MA, USA) overnight at 4°C. Membranes were then rinsed with tris-buffered saline Tween-20 (TBST) 3 times for 5 min and horse radish peroxidase (HRP) labelled goat anti-rabbit second antibody (ab20272, 1: 4000; Abcam, Inc., Cambridge, MA, USA) was added. The membrane was incubated for 2 hrs at room temperature and then rinsed. Relative protein expression was quantified by comparing the gray value of the target band to the internal reference band.
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3

REST Protein Stability Assay

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The KCNK15-AS1 overexpression plasmids were transfected into cells, and CHX (10 ug/ml) was added for incubation for 0, 6, and 12 h. The level of REST in cell lysates were detected by western blot using anti-REST (ab21635, Abcam) antibody. Experiments were repeated three times.
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4

Protein Expression Analysis of Cochlear Tissues

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Cochlear tissues (five mice per sample) were homogenized, and cells were lysed in a RIPA solution containing 0.1% SDS, 50 mM Tris (pH 7.4), 1 mM EDTA (pH 8.0), 1% sodium deoxycholate, 1% TritonX-100, and 200 μM of phenylmethanesulfonyl fluoride (PMSF). The lysis mixture was centrifuged at 13,800 × g for 30 min at 4°C. The supernatant was removed, and the protein concentration was determined using a BCA Protein Assay Kit (#23235, Thermo, CA). Equal amounts of protein (40 μg) were resolved by SDS-PAGE and transferred to a PVDF membrane (#IPVH00010, Millipore, MA). Membranes were blocked with 1× TBST containing 5% dry milk for 2 hr at room temperature and probed with the following antibodies: anti-Kv7.4 antibodies (#ab84820, Abcam; 1:500), anti-REST antibodies (#ab21635, Abcam; 1:1000), or anti-tubulin beta-III antibodies (#MMS-435P, BioLegend; 1:10,000) overnight at 4°C. Then, fluorescent secondary conjugated IgG (#IRDye 800CW goat anti-rabbit IgG [H+L]; #IRDye 800CW goat anti-mouse IgG [H+L], LI-COR Biosciences, NE; 1:10,000) was applied for 90 min at room temperature. All Western blots were quantified using Image Studio software (IS, LI-COR Biosciences).
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5

Protein Expression Analysis by Western Blot

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Total protein was extracted and the concentrations were quantified. Next, the proteins were separated by SDS-PAGE, passed on to PVDF membranes (Millipore, USA). After being sealed in 5% nonfat milk, the membranes were incubated with anti-Bax (ab32503, Abcam, 1/1000), anti-Bcl-2 (ab32124, Abcam, 1/1000), anti-cleaved caspase-3 (ab2302, Abcam, 1/500), anti-E-cadherin (ab40772, Abcam, 1/10000), anti-N-cadherin (ab98952, Abcam, 1/2000), anti-ALKBH5 (ab195377, Abcam, 1/1000), anti-KCNK15 (abs147322, Absin, 1/500), anti-β-catenin (ab32572, Abcam, 1/5000), anti-p65 (ab32536, Abcam, 1/1000), anti-histone H3 (ab1791, Abcam, 1/5000), anti-p-ERK1/2 (ab214362, Abcam, 1/400), anti-ERK1/2 (ab184699, Abcam, 1/10000), anti-NOTCH1 (ab52627, Abcam, 1/1000), anti-HES1 (ab108937, Abcam, 1/500), anti-p-AKT (ab38449, Abcam, 1/500), anti-AKT (ab8805, Abcam, 1/500), anti-PTEN (ab170941, Abcam, 1/1000), anti-FOXP1 (ab32010Abcam, 1/500), anti-EZH2 (ab186006, Abcam, 1/500), anti-REST (ab21635, Abcam, 1/100), anti-MDM2 (ab226939, Abcam, 1/1000), anti-alpha Tubulin (ab7291, Abcam, 1/10000) and anti-GAPDH (ab8245, Abcam, 1/10000) primary antibodies overnight at 4 °C. Next, membranes were hatched with secondary antibody conjugated with horseradish peroxidase. The signals were measured via ECL western blotting substrate (Invitrogen, USA). Each sample was tested in triplicate.
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6

RNA Immunoprecipitation for Gria2 Detection

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Magnetic Beads Protein G were coated with 5 mg of primary antibody in RIP wash buffer (50 mM Tris-HCl, pH 7.4, 150 mM sodium chloride, 1 mM MgCl 2 , and 0.05% NP-40) containing 5% BSA overnight with rotation at 4 C. HEK293 cells expressing HA-MS2P, with Gria1 and Gria2 and Gria2I-MS2 or AK045738-MS2 were collected in 100 mL of RIP lysis buffer (150 mM NaCl, 50 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.1% SDS, 1% NP-40, 0.5% sodium deoxycholate, 0.5 mM DTT, 1 mM PMSF/cocktail) and 10 mL of RNase inhibitor (Ambion, AM2694), and incubated on ice for 10 min. The lysates were then centrifuged at 14,000 rpm for 10 min at 4 C and the nuclear fraction was collected and added with 900 mL of beads-antibody complex in RIP Buffer containing 860 mL RIP wash buffer, 35 mL 0.5 M EDTA, and 5 mL RNase inhibitor, and incubated with rotation overnight at 4 C. 5 mL of the RIP lysate without IP was used as input. After washing, the precipitates were divided into two parts; one was mixed with 5 mL of western blotting sample buffer and incubated for 5 min in boiling water; this blot was used to detect REST/NRSF (1: 1000, Abcam, ab21635). Another was treated with proteinase K at 55 C for 30 min with shaking to digest the protein, followed by DNA extraction and probed with Gria2.
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7

Transcription Factor ChIP-seq and ATAC-seq

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Anti-Flag antibody was used to pull down 3XFLAG tagged-HOXB1 for ChIP-seq experiments. We used the Upstate protocol for ChIP-seq experiments as described in Smith et al [38] (link). All other ChIP-seq experiments were done using specific antibodies against the transcription factors (Anti-PBX: Santacruz; SC-888, Anti-MEIS: Santacruz; SC-25412, Anti-REST: Abcam; ab21635) and histone proteins (Anti-H3K27Ac: Abcam; ab4729, Anti-H3K4me3: Abcam; ab8895). Expression analysis of the genes at various time points (0, 4, 6, 12, 24 and 36 hour) after RA differentiation of ES cells were analysed using RNA-seq [39] (link). Buenrostro and colleagues protocol was used for the chromatin accessibility (ATAC-seq) experiment using approximately 50,000 feeder-free uninduced and differentiated ES cells [40] (link)
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