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The N-PER is a laboratory instrument designed for the extraction and isolation of nuclear proteins from various cell and tissue samples. It utilizes a proprietary extraction buffer system to efficiently separate nuclear proteins from other cellular components, allowing for the study and analysis of these important regulatory biomolecules.

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18 protocols using n per

1

Western Blot Analysis of Neuronal Proteins

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Western blots were performed as previously described (Urraca et al., 2018 (link)). Briefly, protein was extracted from 3-week mature neurons using neuronal protein extraction reagent (N-PER) (Fisher Scientific, Waltham, MA) and protease inhibitor cocktail (Roche). Samples were resolved on a NuPage 1.5mm 4–12% Bis-Tris gel (Invitrogen, Carlsbad, CA) according to manufacturer instructions and transferred to an InvitrolonTM -PVDF membrane (Invitrogen, Carlsbad, CA). The membrane was blocked using Odyssey Blocking Buffer (Licor, Lincoln, NE) for 1 h and incubated overnight at 2–8°C in primary antibody with agitation. Primary antibodies used: anti-MAP2 (Santa Cruz, sc-32791), anti-Nestin (Santa Cruz, sc-23927), and anti-GABA A receptor beta 3 (Abcam, ab98968). anti-GAPDH (Abcam, ab157156) was used as a protein loading control. Blots were incubated at room temperature for 1 h in secondary antibodies for both the 700 and 800 channels using Li-Cor IR secondary antibodies (Licor, 926-32212 and 926-68074). Blots were imaged on a Li-Cor OdysseyTM Fc Imager. Both the 700 and 800 channels were exposed for 2 min.
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2

Western Blot Analysis of Neuronal Proteins

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Western blots were performed as previously described [24] . Briefly, protein was extracted from 3-week mature neurons using neuronal protein extraction reagent (N-PER) (Fisher Scientific, Waltham, MA) and protease inhibitor cocktail (Roche). Samples were resolved on a NuPage 1.5mm 4-12% Bis-Tris gel (Invitrogen, Carlsbad, CA) according to manufacturer instructions and transferred to an Invitrolon TM -PVDF membrane (Invitrogen, Carlsbad, CA). The membrane was blocked using Odyssey Blocking Buffer (Licor, Lincoln, NE) for 1 hour and incubated overnight at 2-8°C in primary antibody with agitation. Primary antibodies used: a-MAP2 (Santa Cruz, sc-32791), a-Nestin (Santa Cruz, sc-23927), and a-GABA A receptor (Abcam, ab98968). a-GAPDH (Abcam, ab157156) was used as a protein loading control. Blots were incubated at room temperature for 1 hour in secondary antibodies for both the 700 and 800 channels using Li-Cor IR secondary antibodies (Licor, 926-32212 & 926-68074) . Blots were imaged on a Li-Cor Odyssey TM Fc Imager. Both the 700 and 800 channels were exposed for 2 minutes.
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3

Trigeminal Ganglion Protein Extraction

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One group of trigeminal ganglions from Tgp35 and wildtype mice was homogenized in neuronal protein extraction reagent (N-PER, Thermo Fisher Scientific) containing protease (cOmplete Mini) and phosphatase (PhosSTOP) inhibitor cocktail tablets (both Roche, Indianapolis, IN). The second group of trigeminal ganglia was homogenized in N-PER containing only the protease inhibitor cocktail, and then treated with Lambda Protein Phosphatase (NEB) for 30min at 30°C. Total protein concentration was measured using a BCA Protein Assay Kit (Cat. No. 23227, Thermo Fisher Scientific). Samples were then sent to Kendrick Laboratories to perform 2D gel electrophoresis.
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4

Protein Extraction and Western Blot Analysis

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Lysis buffer RIPA (Thermo Fisher Scientific) and N-PER (Thermo Fisher Scientific) were used to extract proteins from glioma cells and tissues, respectively. Then, 50 μg total protein per sample was separated using 12% SDS-PAGE and transferred to polyvinylidene fluoride membranes (Thermo Fisher Scientific). The membranes were probed with primary anti-IRAK3 antibody (ab8116, Abcam, MA, USA), anti-MEK1 (phospho S298) antibody [EPR3338] (ab96379), anti-ERK1 + ERK2 antibody [ERK-7D8] (ab54230), anti-c-Fos (phospho T232) antibody (ab17933), and anti-GAPDH antibody [6C5] (ab8245, Abcam) as control. The number of binding proteins was measured using AlphaEaseFC software (Genetic Technologies, FL, USA).
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5

Protein Extraction and Western Blot Analysis

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Proteins were extracted from CP (Additional file 6: Table S3) and lysed in 50 µl of lysis buffer (N-PER; Thermo Fischer Scientific) containing protease inhibitor cocktail (cOmplete ULTRA Mini EDTA-free EASYpack; Roche, Basel, Switzerland). Lysates were clarified by centrifugation at 20,000×g at 4 °C for 10 min, and protein concentrations of the resultant supernatants were determined using BCA Protein Assay Kits (Thermo Fischer Scientific). After 10–15 µg of proteins was heated at 70 °C for 10 min in NuPAGE® LDS Sample Buffer (NP0008; Invitrogen) and NuPAGE® Sample Reducing Agent (NP0009; Invitrogen), samples were electrophoresed on 4–12% NuPAGE® Bis-Tris Mini Gel by NuPAGE® MOPS SDS Running Buffer (20×) (NP0001; Invitrogen) Running Buffer (20×), and then transferred to a polyvinylidene fluoride membrane. Primary antibodies are listed in Additional file 6: Table S3. Signals were detected by chemiluminescence using a WesternBreeze kit (WB7103; Invitrogen). Immunoreactive bands were detected using ImageLab version 4.1 software (Bio-Rad Laboratories, Hercules, CA, USA).
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6

Primary Neuron Isolation and GPR30 Signaling

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Primary cortical neurons were isolated from E18.5 C57/B6 mouse embryos. Briefly, cortical tissues from the brains of the mouse embryos were digested with 0.05 % trypsin‐EDTA.Na2 at 37°C for 12 min and dissociated cortical cells were plated at a density of 1 × 105 on poly D‐lysine‐coated 24‐well plates in Planting Medium (DMEM‐H medium with 10 % [vol/vol] FBS, 1 % [vol/vol] GlutaMAX, and 1 % [vol/vol) penicillin–streptomycin). After 4 h, cells were cultured in Neuron Medium (Neurobasal medium containing 1/50 [vol/vol] B27 and 1 % [vol/vol] GlutaMAX) for another 14 days for screening and maturation in a humidified 5 % CO2 incubator at 37°C.
To determine the signaling pathways of GPR30, cultured cortical neurons were treated with DMSO, GPR30 agonist (G‐1, Cayman Chemical Company, USA) (1 μM), or GPR30 antagonist (G‐15, Cayman Chemical Company, USA) (1 μM) for 1 h for 14 days. After the treatments, cultures were washed with cold PBS (pH 7.2), lysed in cold lysis buffer (N‐PER, Thermo Scientific, MA), and then harvested with a cell scraper, followed by centrifugation at 12,000 rpm for 10 min. Protein concentrations were determined using the BCA Assay (Pierce Biotechnology, IL).
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7

Quantification of Caspase-1 and IL-1β

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Tissue was homogenized using N-PER (Thermo-Fisher Scientific, Waltham, MA, USA) according to the manufacturer's instructions. Protein amounts were quantified using a bicinchoninic acid protein assay (BCA) kit (Thermoscientific, Waltham, MA, USA) according to the manufacturer's instructions. Equal aliquots containing 100 μg amounts of protein were used to determine caspase-1 activity using an enzyme-linked immunosorbent assay (ELISA) according to the manufacturer's instructions (Biovision Inc., Milpitas, CA, USA). In addition, equal aliquots containing 100 μg amounts of protein were used to determine IL-1β protein levels using an ELISA kit according to the manufacturer's instructions (R & D Systems, Minneapolis, MN, USA; sensitivity 4.8 pg/mL).
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8

Primary Hippocampal Neuron Culture Protocol

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Primary hippocampal neuronal cultures were treated at 5 days in vitro (DIV) with respective chemicals for 4 days unless other duration of treatment is indicated. Following the treatment, cultures were washed with cold PBS (pH 7.2), lysed in cold lysis buffer (N-PER, Thermo Scientific, MA)and then harvested with a cell scraper, followed by centrifugation at 10,000 × g for 10 min. Protein concentrations were determined via BCA Assay (Pierce Biotechnology, IL). For tissue protein extraction, 30 mg of hippocampal, cortical and hypothalamic tissue samples were homogenized using a Bullet Blender 24 Homogenizer (Next Advance, NY) in T-PER (Pierce Biotechnology, IL) supplemented with protease and phosphatase inhibitors (Roche Applied Science, IN) and 100 μL 0.5 mm glass beads (Next Advance, NY) at speed 8 for 3 min at 4°C followed by centrifugation at 12,000 rpm for 8 min at 4°C. Supernatants were transferred to new microcentrifuge tubes and protein concentrations were determined via BCA Assay (Pierce Biotechnology, IL).
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9

Western Blot Analysis of Neural Cell Markers

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The differentiated cells or NSCs were lysed (N-PER, Thermo Fisher, USA) and centrifuged at 14,0006 ×g for 20 minutes. Protein concentration of the supernatant was determined using BCA protein assay kit (Beyotime Biotechnology, China). An equivalent amount of protein samples was loaded on SDS-polyacrylamide gels and transferred to PVDF membranes (Millipore, USA). The blots were blocked and subsequently probed with anti-GFAP (1 : 400, Sigma, USA), anti-β-tubulin III (1 : 1500, Sigma, USA), anti-F-actin (Wanlei Biotechnology, China), and anti-Olig2 (1 : 2000; Abcam) overnight. Secondary horseradish peroxidase-conjugated antibodies (1 : 5000; Zhongshan Biotechnology, China) were used and finally, blots were detected with enhanced chemiluminescence (ECL) detection reagents (Thermo Fisher, USA). β-Actin was recognized as the internal control in a parallel running. Bio-Rad Image Lab Software Version 5.2.1 or Image J Version 1.50i was used for optical densities quantification as we did previously [18 (link)]. Separate experiments were conducted for three times.
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10

Murine Brain Protein Extraction and Western Blot

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Protein was isolated from liquid nitrogen shock frozen murine brain-hippocampus tissue using N-Per following the manufacturer’s instructions (Thermo Fisher Scientific, Waltham, MA) and included a protease and phosphatase inhibitor cocktail (Thermo Fisher Scientific, Waltham, MA). Protein was quantified using a 660nm protein assay reagent (Thermo Fisher Scientific, Waltham, MA). 20 μg of protein was denatured at 95°C in Laemmli sample buffer for 5 min. Samples were resolved on a 4–10% polyacrylamide gel and transferred to nitrocellulose membranes, which were blocked for 1h at room temperature in either 3% BSA / TBST. The membranes were incubated in primary antibody overnight at 4°C. The primary antibodies used were rabbit polyclonal PER2 (AB2202, Millipore Sigma, Burlington, MA; antibody verified for PER2 specificity [35 (link)]), mouse monoclonal β-actin (8H10D10, Cell signaling, Danvers, MA), The secondary antibodies used were goat anti-rabbit IgG (Thermo Fisher Scientific, Waltham, MA) and goat anti-mouse IgG (Thermo Fisher Scientific, Waltham, MA).
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