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11 protocols using anti calnexin

1

Pharmacological Inhibitors and Antibodies for Signaling Analysis

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The pharmacological inhibitors BIX02189 and WNK463 were obtained from Selleckchem (Houston, TX, USA) and trametinib from LC Laboratories (Woburn, MA, USA). General chemical reagents were purchased from Sigma–Aldrich (St Louis, MO, USA), Merck (Darmstadt, Germany) or BD Biosciences (San Jose, CA, USA).
The antibodies were obtained as follows: anti‐MEK5 was from Enzo Life Sciences (Farmingdale, NY, USA); anti‐GAPDH and anti‐ERK1/2 from Santa Cruz Biotechnology (Santa Cruz, CA, USA); anti‐pERK1/2, anti‐MEK1/2, anti‐pMEK1/2, anti‐WNK1 and anti‐MEKK2 from Cell Signaling Technologies (Danvers, MA, USA); anti‐Calnexin from Stressgen Bioreagents (Victoria, BC, Canada); anti‐Ki‐67 (clone SP6) from Vitro Master Diagnostica (Granada, Spain); anti‐pWNK1 from R&D Systems (Minneapolis, MN, USA); and horseradish peroxidase‐conjugated secondary antibodies were from Bio‐Rad Laboratories (Hercules, CA, USA). Antibodies raised against ERK5, pERK5 or pMEK5 were developed in our laboratory and have been described.19, 25, 26 The pERK1/2 antibody conjugated to PE fluorophore was obtained from Biolegend (San Diego, CA, USA) and the anti‐pERK5 conjugated to AF488 from Santa Cruz Biotechnology (p‐ERK 5 Antibody (1.T218/Y220) Alexa Fluor®488, sc‐135760 AF488).
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2

Orai1 and STIM2 Expression Profiling in Immune Cells

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All cells were maintained in a 37 °C, 5% CO2 humidified incubator in corresponding medium, namely, minimum essential medium for HEK293 WT (HEK) and stably expressing Orai1 (HEKO1), AMIV for human CD4+ cells and RPMI 1640 for E6.1 Jurkat T (Jurkat) cells. All media were supplemented with 10% fetal calf serum and 1% penicillin–streptomycin and HEKO1 were maintained in 1 μg ml−1 puromycin. HEK cells were passaged by treatment with trypsin/EDTA. For transfection, the indicated amount of DNA was electroporated into HEK cells and Jurkat cells with Nucleofector II or into CD4+ cells with 4D Nucleofector core unit according to the manufacturer's instructions 16–20 h before measurements. Human Orai1, Orai2 and STIM1 were subcloned into the EcoRV site of either RFP pMAX, or IRES-RFP-pCAGGS. STIM2.2 was purchased with an N-terminal CFP or YFP tag (Addgene). We used this cDNA (STIM2.2: pEX-CMV-SP-YFP-STIM2) and two complementary primers (see Supplementary Table 1) each encoding part of the exon 9 sequence to insert the desired nucleotides into the exon 8/10 boundary. All constructs were confirmed by sequencing. Antibodies used in this study were anti-His Tag (Cell Signaling, 2366, 1:1,000); anti-STIM2 (C-term, Sigma, #S8572, 1:2,000); anti-Calnexin (Stressgen, #SPA-865, 1:1,000) and anti-γ-tubulin (Cell Signaling, #5886, 1:1,000).
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3

Cell Viability and Protein Expression Assay

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Cell culture media, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), hematoxylin and eosin were purchased from Sigma. Foetal bovine serum (FBS) and antibiotics were from Life Technologies and Immobilon P (PVDF) membranes from Millipore. OOS was provided by Catalysis, S.L. (Madrid, Spain). The Cytometric Bead Array Mouse Inflammation kit was purchased to BD biosciences. Other generic chemicals were purchased from Sigma Chemical Co., Roche Biochemicals or Merck.
The origin of the different antibodies used in the Western blotting analyses were as follows: the anti-GAPDH, anti-p21, anti-Wee1, anti-CDC2/CDK1, anti-pCDC2, anti-Cyclin B and anti-Cyclin D1 antibodies were purchased from Santa Cruz Biotechnology; the anti-BUBR1, anti-Rb, anti-Cyclin A, anti-Cyclin D3 and anti-Cyclin E from BD Biosciences; the anti-p27 and the anti-pRbS780 from Cell Signaling technology; the anti-Calnexin from Stressgen and the anti-pHistone H3 from Millipore. The horseradish peroxidase-conjugated secondary antibodies were from Bio-Rad.
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4

Cloning and Expressing MPP1-GFP Mutant

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The MPP1-green fluorescent protein (GFP) construct was obtained by cloning the MPP1 gene sequence into the pEGFP-C1 vector (Invitrogen, Waltham, MA) using BamHI and XhoI restriction sites. To obtain a MPP1 rescue mutant (MPP1-R), the MPP1 sequence was cloned into the p3XFLAG-CMV-10 vector (Sigma, St. Louis, MO) using HindIII and BamHI restriction sites and subsequently modified by introducing four silent mutations in the region recognized by the shRNA sequence using site-directed mutagenesis (Stratagene, Waltham, MA) (primer sequence: 5′ GGAGATGACGAGGAACATTAGCGCCAATGAGTTCTTG 3′). Abp140-17aaRuby-nos1-3′ UTR (lifeAct-Ruby) construct was a gift from M. C. Lecomte U665 INSERM Paris. Transient transfections of HEL cells were performed by CLB (Lonza, Basel, Switzerland) electroporation. Mouse monoclonal anti-MPP1 antibodies were purchased from Abnova (Taipei, Taiwan), anti-actin and anti-GFP antibodies (SantaCruz Biotechnology, Dallas, TX), anti-Flag (Sigma), anti-Flotillin-1 (Abcam, Cambridge, UK), anti-Furin Convertase (Thermo Fisher Scientific, Waltham, MA), anti-Calnexin (Stressgen, San Diego, CA).
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5

Immunoblot analysis of protein markers

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The following antibodies were used for immunoblot analysis: anti-Flag M2 (1:1000 dilution; Sigma), anti-Myc (1:2000 dilution; Abcam and Santa Cruz), anti-tubulin (1:5000 dilution; Sigma), anti-Calnexin (1:1000 dilution; Stressgen), anti-Cox-1 (1D6) (1:1000 dilution; Invitrogen), and anti-FACL4 (1:200 dilution; Abgent).
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6

Western Blot Analysis of EV Proteins

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Cells were recovered by centrifugation and pellets were resuspended in lysis buffer (62 mM Tris–HCl pH 6.8, 11% glycerol, 1% SDS containing phosphatase and protease inhibitors) and sonicated to prepare cell lysates.
Aliquots of cell lysates (15 μg proteins) or EVs (2 μg proteins) were mixed with sample buffer 5X (1 M Tris–HCl pH 6.8, 5% (w/v) SDS, 6% (v/v) glycerol, 0.01% (w/v) Bromophenol blue). Samples were electrophoresed on 12% acrylamide gel and electrotransferred to PVDF membrane. After blocking, membranes were incubated overnight with the following primary antibodies: anti-Alix (Santa Cruz, USA), anti-CD63 (Cymbus Biotechnology, UK), anti-β-actin (Sigma-Aldrich, USA), (Santa Cruz, USA), anti-calnexin (Stressgen, USA), anti-flotillin (BD Biosciences, Franklin Lakes, USA), anti-Apo B (EMD Millipore Corp, USA). HRP-linked secondary antibodies (GE Biosciences, Piscataway, USA) were probed according to manufacturer’s instructions. Immunoblots were detected by chemiluminescence using ECL system (GE Biosciences).
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7

Antibody Dilution Rates for TorsinA, TorsinB, LAP1, and LULL1

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The dilution rates for each antibody used in this study are listed as follows. anti-torsinA (rabbit polyclonal, Abcam; 1:10,000); anti-torsinB (rabbit polyclonal; kind gifts of Dr. Rose Goodchild; VIB Center for the Biology of Disease and Dr. Christian Schlieker, Yale University; 1:1000); anti-LAP1 and anti-LULL1 (rabbit polyclonal; kind gift of Dr. Christian Schlieker; Yale University; 1:1000); anti-calnexin (rabbit polyclonal, Stressgen; 1:10,000); anti GAD65/67 (rabbit polyclonal, Millipore; 1:2000); anti-neurofilament-M (rabbit polyclonal, Millipore; 1:200); γ-tubulin (monoclonal, Sigma; 1:2000); anti-NeuN (Monoclonal A-60, Millipore; 1:200); anti-GABA (rabbit polyclonal, Sigma, 1:200); anti-GFP (rabbit polyclonal, Abcam; 1:200); Goat anti-Rabbit IgG Horse Radish Peroxidase and Goat anti-Mouse IgG Horse Radish Peroxidase (Cell signaling; 1:10,000); anti-mouse Alexa Fluor 488, anti-rabbit Alexa Fluor 488, and anti-rabbit Alexa Fluor 633 (Invitrogen; 1:400).
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8

Hippocampal Membrane Protein Extraction

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The hippocampi were extracted and homogenized as previously described (Nissenkorn et al., 2019 (link)). Briefly, 0.45–0.7 mg of tissue was homogenized in 0.32 M sucrose supplemented with protease inhibitors (Sigma-Aldrich, St. Louis, MO, USA), 1 mM EDTA and 1 mM PMSF, pH 7.4. Crude membrane preparation was produced by centrifugation at 27,000 × g for 75 min. The pellet was solubilized in 150 mM NaCl, 2% Triton X-100, 25 mM Tris, supplemented with protease inhibitors, 1 mM EDTA and 1 mM PMSF, pH 7.4. 50 μg aliquots of total protein were separated on Tris-acetate gel (6%) and transferred onto PVDF membrane. After overnight blocking in 5% non-fat dry milk in Tris-buffered saline (TBS), the membrane was incubated overnight with anti-NaV1.1 antibody (1:200, Alomone Labs, Jerusalem, Israel; Catalog# ASC-001) or anti-calnexin (1:2,000, Stressgen Biotechnologies, San Diego, CA, USA), followed by 2 h incubation with HRP-conjugated goat anti-rabbit antibody (1:10,000, Sigma-Aldrich, St. Louis, MO, USA). The signal was visualized by chemiluminescent detection using ECL.
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9

Western Blot Antibody Reagents

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Anti-firefly luciferase (Abcam, Cambridge, UK; ab187340, 1:4000), anti-GAPDH (CST, Danvers, USA; #2118, 1:1000), anti-calnexin (Stressgen, San Diego, USA; SPA-860, 1:1000), anti-Sec61α (Sigma Aldrich, St. Louis, USA; SAB2500917, 1:1000), anti-β-actin (CST, #4970, 1:1000), anti-FLAG M2 (Sigma Aldrich, St. Louis, USA; F1804, 1:1000), anti-α-1antitrypsin (DAKO, Glostrup, Denmark; A0012, 1:1000), anti-IRE1α (CST, #3294, 1:1000), anti-PERK (CST, #3192, 1:500), anti-CHOP (CST, #2895T, 1:500), anti-IgG (H+L chain) (Rabbit) pAb-horseradish peroxidase (HRP) (MBL, Tokyo, Japan; 458, 1:5000), peroxidase AffiniPure goat anti-mouse IgG (H+L) (Jackson Immuno Research Laboratories, West Grove, USA; 115-035-003, 1:5000), anti-rabbit IgG, HRP-linked antibody (CST, 7074, 1:3000), and anti-mouse IgG, HRP-linked antibody (CST, 7076, 1:3000) were purchased. Anti-Sec61β (1:1000) was a kind gift from Dr Tom A. Rapoport (Harvard Medical School, Boston, USA). Anti-ERP57 antibody (1:1000) was generated in our laboratory (Sopha et al., 2012) .
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10

Antibody Sources for GFP, RFP, and PrP-A

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Rabbit antisera for GFP and RFP were made as described (Stefanovic and Hegde, 2007 ) and rabbit antisera for Tmp21 was made by immunizing rabbits with a peptide corresponding to the cytoplasmic tail (CLRRFFKAKKLIE) conjugated to keyhole limpet hemacyanin via the terminal cysteine. The PrP-A antibody was previously described (Rane et al., 2004 (link)). The antibody against TCR-α, A2B4, (gift from Carolyn Suzuki) was previously described (Suzuki et al., 1991 (link)). CHOP and XBP-1 antibodies were gifts from Linda Hendershot.
Purchased antibodies included anti-calnexin (StressGen SPA-860), anti-Grp94 (StressGen SPA-850), anti-ERGIC53 (Santa Cruz SC-66880), anti-alpha tubulin (Sigma T6199), anti-GAPDH (Santa Cruz SC-20357), Cy5-conjugated anti-rabbit IgG (Jackson ImmunoResearch 111-175-003) and Alexa 488 goat anti-mouse Ab (Invitrogen A11029).
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