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13 protocols using anti p ire1α

1

Analyzing Endoplasmic Reticulum Stress Pathways

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Tunicamycin was purchased from Sigma-Aldrich (St. Louis, MO, USA). Chloroquine and bafilomycin A1 were from MBL (Nagoya, Japan). The following primary antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA): anti-IRE1α, anti-XBP1s, anti-FoxO1, anti-full length and cleaved caspase-3, anti-HDAC1, anti-GAPDH and anti-β-actin antibodies. The anti-XBP1u antibody was obtained from Santa Cruz Biotechnology, Inc (Dallas, TX, USA). Anti-LC3 antibody was purchased from MBL. Anti-p-IRE1α was from Abcam (Cambridge, UK). Anti-goat mouse and anti-rabbit antibodies were from Santa Cruz Biotechnology, Inc and Cell Signaling Technology, respectively. Small interfering RNA (siRNA) for XBP1, IRE1α and control siRNA were from Santa Cruz Biotechnology, Inc. FoxO1 siRNA were from Cell Signaling Technology. Cytoplasmic & Nuclear Protein Extraction Kit was from 101 Bio (Palo Alto, CA, USA).
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2

Western Blot Analysis of UPR Markers

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Western blot was performed as previously described76 (link). Briefly, protein lysates were separated by SDS polyacrylamide gel electrophoresis and transferred onto a PVDF membrane. Membranes were incubated overnight at 4 °C with each primary antibody, including anti-GRP78 (sc-1050, Santa Cruz Biotechnology, TX USA), anti-IREa (#3294, Cell Signaling Technology, MA USA), anti-p-IRE1α (#ab48187, Abcam, UK), anti-p-eIF2α (#3398, Cell Signaling Technology, USA), anti-ATF4 (sc-200, Santa Cruz Biotechnology, TX USA), anti-p-Stat3 (#9145, Cell Signaling Technology, MA USA), anti-GAPDH (sc-25778, Santa Cruz Biotechnology, TX USA) and anti-Tubulin (#2144, Cell Signaling Technology, MA USA). Then the membrane was incubated in 5% non-fat milk containing HRP-conjugated secondary antibody (1:5000) for 1 h. Signals were detected by ECL Chemiluminescent kit (Millipore).
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3

Western Blot Analysis of Neuronal Signaling

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Primary cortical neurons or brain tissues were lysed with RIPA buffer containing phosphatase and protease inhibitors. After measurement with BCA kits, the proteins were denatured by boiling for 10 min and then loaded on 8-12% SDS‒PAGE gels, followed by transfer from the gels to activated PVDF membranes. After blocking with 5% nonfat dry milk, the membranes were incubated with the following primary antibodies: anti-PI3K (ab154598, 1:2000), anti-p-Akt (ab38449, 1:1000), anti-Akt (ab283852, 1:2500), anti-GRP78 (ab21685, 1:3000), anti-p-PERK (ab192591, 1:1000), anti-PERK (ab79483, 1:2500), and anti-p-IRE1α (ab124945, 1:2500) were obtained from Abcam, USA and anti-IRE1α (#3294, 1:2500), anti-ATF6 (#65880, 1:2000), anti-CHOP (#5554, 1:2000), anti-Caspase12 (#35965, 1:2500), anti-Caspase3 (#9579, 1:1000), anti-Bcl-2 (#3869S, 1:2000) and anti-Bax (#5023, 1:2500) were supplied by Cell Signaling Technology, U.S.A. Anti-β-actin antibody (GB15004, 1:3000) was purchased from Servicebio Technology (China). After incubation with the primary antibodies overnight, the membranes were washed three times with TBST and incubated with secondary anti-rabbit HRP antibody (GB1213, 1:5000, Servicebio Technology, China). Enhanced chemiluminescence was used to visualize the membranes, and the analysis was performed using ImageJ software.
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4

DHA Modulates Lipid Metabolism Pathways

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DHA (purity ≥ 98%), Oil Red O, tunicamycin, insulin, dexamethasone, rat-tail collagen and type IV collagenase were purchased from Sigma-Aldrich (Sigma-Aldrich, St. Louis, MO, USA). Briefly, the stock solution of DHA was dissolved in 95% ethanol at a concentration of 200 mM, and the working solution was prepared by adding the stock to the culture medium to achieve a final concentration of 25 μM. Epidermal growth factor was a product from Peprotech (Peprotech, Rocky Hill, NJ, USA). The primary antibodies applied in this study were anti-GRP78 (Cell Signaling Technology, Danvers, MA, USA), anti-ACC (Cell Signaling Technology, Danvers, MA, USA), anti-IRE (Santa Cruz Biotechnology, Santa Cruz, CA, USA), anti-ACOX1 (Abcam, Cambridge, UK), anti-p-IRE1α (Abcam, Cambridge, UK) and anti-β-actin (Beyotime, Shanghai, China).
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5

Characterization of ER Stress Pathway

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Lysis buffer was used to lyse treated cells. Samples with identical levels of total protein were evaluated and then transferred after that, analyzed with the imaging system after electrophoretic transfer. The following antibodies were applied: anti-BIP (CST, C50B12), anti-CHOP (CST, L63F7), anti-p-PERK CST, D11A8), anti-PERK (CST, 16F8), anti-eIF2α (CST, D7D3), anti-p-eIF2α (CST, D9G8), anti-ATF4 (proteintech, 10835-1-AP), anti-Ero1-Lα(CST, 3264T), anti-Cyt C (proteintech, 10993-1-AP), anti-JNK (CST, 9252T), anti-p-JNK (CST, 9251S), anti-XBP1s (CST, E9V3E), anti-IRE1α (CST, 3294T), anti-p-IRE1α (Abcam, ab124945).
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6

Immunofluorescence Imaging of p-IRE1α

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After appropriate treatment, cells were fixed using 4% paraformaldehyde, permeabilized for 15 min with 0.1% Triton X‐100, and blocked for 30 min with 5% goat serum. Following incubation overnight with anti‐p‐IRE1α, 1:150, Abcam, UK at 4°C, cells were probed with secondary Cy3‐ or AF488‐conjugated anti‐IgG (1:100, Shanghai biyuntian Biotechnology Co., Ltd, China) for 90 min. Cells were then washed thrice with PBS, counterstained for 5 min with DAPI (4,6‐diamidino‐2‐phenylindole dihydrochloride), and imaged with a laser fluorescence microscope (Olympus, Tokyo, Japan). All data were analysed by an investigator blinded to experimental groupings.
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7

Comprehensive Immunoblotting Analysis of Cellular Pathways

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Western blotting (WB) was performed as previously described [14 (link)]. Antibodies used were as follows: anti-acetylated lysine, anti-GRP78/BiP, anti-HDAC6, anti-HDAC9, anti-PERK and p-PERK, anti-p-eif2α, anti-IRE1α, anti-FYN, anti-eif2α, anti-p-eif2α, anti-BTK, anti-p-BTK, anti-PCL-ɣ2, anti-p-PCL-ɣ2, anti-CARD11, anti-ATF4, anti-AKT, anti-p-AKT, anti-CHOP, anti-Helios, anti-β-actin, anti-BIM (C23C5), anti-Bcl2 (Cell Signaling Technology); anti-MAPK10, anti-p-IRE1α and anti-SH3BP5 (Abcam); anti-XBP-1 (Santa Cruz). Densitometry analysis was performed on scanned images using ImageJ software (NIH).
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8

ER Stress Pathway Protein Analysis

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Cell or tissue lysates were extracted in RIPA buffer (Beyotime, Cat# P0013B) Protein concentration was evaluated by bicinchoninic acid (BCA) Protein Assay Kit (Thermo Fisher Scientific, Cat# 23227) and then analyzed by SDS–PAGE gel electrophoresis and blotting onto PVDF membranes. Primary antibodies used included: anti-ERO1L (Abcam, Cat# ab177156), anti-IRE1α (Abcam, Cat# ab37073), anti-pIRE1α (Abcam, Cat# ab48187), anti-XBP1s (Cell Signaling Technology, Cat# 12782), anti-PERK (Abcam, Cat# ab229912), anti-pPERK (Cell Signaling Technology, Cat# 3179), anti-eIF2α (Cell Signaling Technology, Cat# 9722), anti-peIF2α (Cell Signaling Technology, Cat# 9721), anti-ATF4 (Cell Signaling Technology, Cat# 11815), anti-ATF6α (Santa Cruz, Cat# sc-166659), anti-CHOP (Santa Cruz, Cat# sc-7351), and anti-β-Actin. Primary antibodies were applied in 5% non-fatty milk or primary antibody dilution (Beyotime, Cat# P0256) in TBST and incubated overnight at 4°C, followed by HRP-conjugated secondary antibodies incubation at room temperature for 2 h. Secondary antibodies used included: Goat anti-Rabbit HRP-conjugated IgG (Abcam, Cat# ab6721), Rabbit anti-Mouse HRP-conjugated IgG (Abcam, Cat# ab6728). Images were collected by Amersham Imager 600 (General Electric).
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9

Western Blot Analysis of ER Stress Markers

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Lysates of CL tissue from each stage were prepared in PRO-PREP protein lysis buffer (iNtRON, Daejeon, Korea). The protein concentration for each sample was estimated using a Bradford dye-binding assay with bovine serum albumin (BSA) as a standard (Bradford, 1976). Aliquots of the proteins (30 μg) were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) on 12% gels. After electrophoresis, the separated proteins were transferred onto nitrocellulose (NC) membranes (Pall Corporation, Port Washington, NY, USA). After blocking with 5% non-fat milk in Tris-buffered saline (TBS) with 0.1% Tween 20 at 4 °C under mild agitation, the membranes were incubated with 1:2000 diluted anti-CHOP, anti-p90ATF6, anti-CREB-2, anti-3β-HSD (Santa Cruz, Biotechnology, CA, USA), anti-GRP78/BIP, anti-p-eIF2α, anti-IRE1, anti-eIF2a, anti-JNK, anti-p-SAPK/JNK, anti-caspase-3, anti- β-tubulin (Cell Signaling, Beverly, MA, USA), anti-p50ATF6 (IMG, San Diego, CA, USA), and anti-p-IRE1α (Abcam, Cambridge, MA, USA) antibodies. The membranes were then incubated with secondary horse radish peroxidase (HRP)-conjugated anti-goat/mouse/rabbit IgG (Thermo, Rockford, IL). Antibody binding was detected using an enhanced chemiluminescence (ECL) kit (Advansta, CA, USA). Band intensities were quantified using the Image J software (NIH, MD, USA).
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10

ER Stress Pathway Activation in Lung Tissues

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Right upper lung tissues and A549 cells were lysed with protein extraction reagent (P0013; Beyotime Institute of Biotechnology) according to the manufacturer's protocol. Protein concentration was determined using BCA protein quantification kits (ab102536; Abcam). Proteins (30 µg proteins in each group) were separated by 12% gradient SDS-PAGE and were transferred to polyvinylidene fluoride membranes. Nonspecific binding was blocked with 10% non-fat dry milk in Tris-buffered saline (TBS) at room temperature for 1 h. The membranes were then incubated overnight at 4°C with anti-PERK (1:1,000 dilution), anti-p-PERK (1:1,000 dilution), anti-GRP78 (1:1,000 dilution), anti-JNK (1:1,000 dilution), anti-p-JNK (1:1,000 dilution), anti-CHOP (1:1,000 dilution), anti-IRE1α (1:1,000 dilution), anti-p-IRE1α (1:1,000 dilution), anti-p-50ATF6α (1:1,000 dilution), anti-cleaved caspase-3 (1:1,000 dilution) and anti-GAPDH (1:1,000 dilution; ab8245; Abcam). After washing with TBS containing 20% Tween-20 (20% Tween-20: TBS =2.6:1,000), the membranes were incubated with an HRP-labeled goat anti-rabbit IgG secondary antibody (1:7,500 dilution; A0208; Beyotime Institute of Biotechnology) at room temperature for 1.5 h. The blots were visualized using an enhanced chemiluminescent detection system (Bio-Rad, Hercules, CA, USA).
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