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7 protocols using ap136p

1

Quantifying Cell Surface Expression of hK2P17.1

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For quantification of cell surface expression, hK2P17.1 constructs harboring an extracellular HA tag were expressed in Xenopus oocytes. Cells were incubated for 30 min at 4°C in standard oocyte-maintaining solution (SOS) containing 1% bovine serum albumin (BSA) to block nonspecific binding of antibodies. Labeling was performed with monoclonal rat anti-HA antibody (clone 3F10, Roche; 1 mg/ml) in 1% BSA/SOS for 60 min at 4°C. After repeated washing steps, cells were incubated with peroxidase-conjugated goat anti-rat secondary antibody (AP136P, Sigma Aldrich, 1:10,000) diluted in 1% BSA/SOS for 60 min at 4°C. Oocytes were washed thoroughly for 60 min at 4°C in SOS without BSA and placed in Amersham ECL-Prime Western blotting detection reagent (GE Healthcare). Chemiluminescence was detected by a FluorChem Q luminescence detector (Cell BioSciences) and quantified using ImageJ software version 1.51f (Schneider et al., 2012 (link)). Uninjected oocytes served as negative controls.
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2

Comprehensive Protein Profiling Protocol

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NR2F2 Isoform 1 (41859, Abcam for western blot (1:1000)); 61214, Active Motif for ChIP (5 μL per sample), NR2F2 Isoform 2 (Millipore custom antibody (1:1000)), SNAIL (3879, Cell Signaling Technology (1:1000)), Actin (A3854, Sigma (1:50,000)), Lamin-B (sc6217, Santa Cruz (1:50,000)), Alpha-tubulin (T9026, Sigma (1:50,000)). Rabbit secondary (Sigma, A0545 (1:20,000)), mouse secondary (Sigma, A9044 (1:20,000)), rat secondary (Millipore, AP136P (1:20,000)), and goat secondary (Sigma, A5420 (1:20,000)).
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3

IgY Purification and Characterization

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Stain-free 4%-20% SDS PAGE (Criterion TGX Stain-Free Protein Gel; #5678094; BioRad, Hercules, CA) and Western Blot analysis were used to characterize the purified IgY. The two primary antibodies used were: rat anti-IgY (Sapphire, LO-IgY-16, batch: 10332, Ann Arbor, Michigan), diluted 1:500 and mouse anti-ovalbumin (Abcam; ab17293, lot number: GR3376118; Cambridge, MA) diluted 1:500, followed by goat anti-rat HRP (EMD Millipore; AP136P, Lot. Number: 3660343; Billerica MA) Cat. No: NA931V (Rock Immunochemicals; RL610603002, Lot. No: 17041904; Pottstown, PA) and sheep anti-mouse HRP, respectively.
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4

Immunoblotting Protocols for Autophagy Markers

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Immunoblots were performed as described elsewhere [55]. The primary antibodies used are presented in Table 2. Membranes were analyzed using the appropriate peroxidase-conjugated secondary antibodies (Life Technologies, A15999; Amersham, NA931 and NA934; Merck Millipore, AP136P). Proteins were detected by enhanced chemiluminescence (GE Healthcare, RPN2232).10.1080/15548627.2018.1474992-T0002

Antibodies used in immunoblots, immunofluorescence and ChIP.

AntibodySourceCatalog numberDilution
NFE2L2/NRF2Cuadrado lab-1:2000 (WB)
HMOX1Enzo Life SciencesOSA1101:2000 (WB)
SQSTM1/p62Sigma AldrichP00671:2000 (WB)
MmLAMP2A/Igp96Zymed/Invitrogen51–22001:1000 (WB). 1:100 (ICF)
HsLAMP2AAbcamab185281:1000 (WB)
LAMP2BCuervo lab-1:1000 (WB)
LAMP2CCuervo lab-1:1000 (WB)
LAMP1 (1D4B)Hybridoma Bank1D4B1:1000 (WB). 1:250 (ICF)
RNASERockland Immunochemicals100–1881:5000 (WB)
HSPA8/HSC70 (13D3)Novus BiologicalsNB12027881:5000 (WB)
ACTBSanta Cruz Biotechnologysc-16161:5000 (WB)
LMNB/lamin BSanta Cruz Biotechnologysc-62171:5000 (WB)
GAPDHCalbiochemCB10011:5000 (WB)
LC3BCell Signaling Technology27751:2000 (WB)
V5Life Technologies37–75001:250 (ChIP)
IgG2aAbcamab184131:250 (ChIP)

ICF, immunocytofluorescence. WB, western blot. ChIP, chromatin immunoprecipitation.

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5

Quantifying CD14 Expression in Cell Lines

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The two cell lines were tested for their basal Cd14 expression and expression after stimulation with LPS (0.1 ng/ml, Sigma-Aldrich, Munich, Germany) for 12 hours. Proteins were isolated from the cells by using NP40 buffer (1 mM PMSF, 1 mM DDT, 1 mM sodium ortho-vanadate, Complete Mini Protease inhibitor cocktail tablet [Roche Applied Science, Mannheim, Germany]) and concentrations were defined by performing Bradford assays. 50 μg protein were used for SDS-PAGE followed by a semi-dry transfer to Optitran BA-S 85 membrane (Sigma-Aldrich, Munich, Germany) using Semi-Dry Blotter Maxi V20-SDB (Carl Roth, Karlsruhe, Germany) and transfer buffer (39 mM glycine, 0.037% SDS, 48 mM Tris, 20% methanol). Primary antibodies were applied to bind to CD14 (rat monoclonal [Sa14-2] to CD14 [FITC], Abcam, Cambridge, UK) or to beta actin (mouse monoclonal [mAbcam 8226] to beta Actin, Abcam). After labeling CD14 antibody with goat anti rat IgG [HRP] (AP136P; Millipore, Billerica, USA) and beta actin with F(ab’) 2 rabbit anti mouse IgG [HRP] (STAR21B; AbD serotec, Oxford, UK) as secondary antibodies, luminescence of the different bands was activated by using Roti-Lumin 1 and 2 solution (Carl Roth). Detection of the bands was performed by x-ray film (GE Healthcare, Munich, Germany)
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6

Immunocytochemical Characterization of HMSCs

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At passage 3, HMSCs were trypsinized, washed, and resuspended in mesenchymal stem cell medium (PromoCell, C-28010) at a concentration of 1 × 105 cells/mL. HMSCs were fixed with paraformaldehyde at 4°C for 15 min and washed with distilled water before permeabilization in 0.5% Triton-X100. Non-specific binding was blocked using blocking solution (PBS containing 1% bovine serum albumin (BSA)) for 1 hour at room temperature. HMSCs were then incubated 2 hours at room temperature with primary antibodies from rabbit against antigrowth associated protein-43 (GAP-43, 1 : 200) (Chemicon, AB5220) and against antiglial fibrillary acidic protein (GFAP, 1 : 500) (Chemicon, AB5804) and from mouse against antineuronal nuclei (NeuN, 1 : 100) (Chemicon, MAB377). After washing, HMSCs were incubated 15 minutes with goat anti-rat IgG (Millipore, AP136P) and goat anti-rabbit IgG (Millipore, 12-348MN) secondary antibodies. After several washes in PBS, HMSCs were incubated with horseradish peroxidase (HRP-) coupled streptavidin for 10 min. DAB (diaminobenzidine) served as chromogen (Figure 2).
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7

Western Blot for DNMT3B Protein

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Total protein extract was obtained using RIPA buffer. Samples were subjected to electrophoresis in fast cast SDS-PAGE gels according to the manufacturer’s protocol (Bio-Rad). Next, the separated proteins were transferred onto an TransBlot Turbo Polyvinylidene Fluoride (PVDF) membrane using a Trans-Blot Turbo Transfer System (Bio-Rad). PVDF membranes were imaged on the Bio-Rad ChemiDoc imaging system to verify transfer. Membranes were blocked in EveryBlot Blocking Buffer for 5 min at room temperature and then incubated overnight at 4 °C with the primary monoclonal antibody, anti-DNMT3B (1:2000; MABE305, Millipore). The membranes were then incubated for 1 h at room temperature with secondary antibody horseradish peroxidase-conjugated anti-rat IgG (1:5000; AP136P, Millipore). After incubation, the blots were imaged on a Bio-Rad ChemiDoc imaging system in order to measure total protein content as a loading control for protein normalization, as previously described [36 (link)]. Membranes were developed with the Clarity Western ECL Substrate (Bio-Rad), chemiluminescent signals were acquired on ChemiDoc MP (Bio-Rad) and band intensities were analyzed using Image Lab software (Bio-Rad).
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