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19 protocols using ab203119

1

Revealing ER Stress and Autophagy Markers

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Following the desired treatments, CHO cells were washed and harvested on ice, and then lyzed with ice-cold protein extraction buffer (Beyotime, Nanjing, China). The protein concentration was determined using BCA protein assay kit (ComWin, Beijing, China). Equal amounts of protein were loaded into gel wells, separated by electrophoresis on SDS-polyacrylamide gels and transferred onto PVDF transfer membrane (Millipore, Bedford, MA). The transferred blots were blocked with blocking agents (5% w/v BSA and 0.05% Tween-20 in TBS) for 1 h at room temperature. Blots were then incubated in a certain proportion of specific primary antibodies: anti-GRP78 (ab25192 Rabbit monoclonal, Abcam), anti-ATF-6 (ab203119 Rabbit polyclonal, Abcam), anti-PERK (C33E10 Rabbit polyclonal, Abcam), anti-IRE1 (ab37073 Rabbit polyclonal, Abcam), anti-CHOP (ab11419 Mouse monoclonal, Abcam), anti-Beclin1 (ab55878 Rabbit polyclonal, Abcam), anti-LC3B (ab81785 Rabbit polyclonal, Abcam) (1:1000) overnight at 4°C. These membranes were rinsed 3 times for 10 min each with TBS-Tween (Sigma, St. Louis, MO, USA) and incubated with HRP conjugated secondary antibodies (1:5000) (CWBio, Beijing, China). After washing, protein bands were visualized by an enhanced chemiluminescence detection kit (ComWin, Beijing, China). Each band density was quantified using Image J software (GE Healthcare, Piscataway, New Jersey, USA).
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2

ER Stress Pathway Molecular Markers

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The primary antibodies used are listed as follows: anti-cytochrome c (1:1,000, 10993-1-AP, Proteintech, rosemont, IL, USA), anti-caspase-9 (1:1,000, #9508, Cell Signaling, Danvers, MA, USA), anti-PERK (1:1,000, #3192, Cell Signaling, Danvers, MA, USA), anti-phosphorylated-PERK (anti-p-PERK; Thr982;1:800, DF7576, Affinity Biosciences, Cincinnati, OH, USA), anti-IRE1 (1:500, ab37073, Abcam, Cambridge, MA, USA), anti-p-IRE1 (phosphor S724; 1:1,000, ab48187, Abcam, Cambridge, MA, USA), anti-activating transcription factor 6 (anti-ATF6; 1:1,000, ab203119, Abcam, Cambridge, MA, USA), anti-N’ATF6 (1:800, ab37149, Abcam, Cambridge, MA, USA) and anti-β-actin (1:3,000, GTX109639, GeneTex, Irvine, CA, USA). The ER stress activator Tunicamycin (TM) and the p-PERK inhibitor GSK2656157 were obtained from MedChem Express (Monmouth Junction, NJ, USA). The p-IRE1 inhibitor 3,5-dibromosalicylaldehyde (DBSA) was obtained from Tokyo Chemical Industry (TCI, Tokyo, Japan).
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3

Immunohistochemical Analysis of ER Stress Markers

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The OSCC samples were analyzed immunohistochemically using antibodies against PERK (Abcam, Cat No: ab65142), ATF6 (Abcam, Cat No: ab203119), or GRP78 (Abcam, Cat No: ab21685). Next, the brief deparaffinization of 4-μm sections was made in xylene, followed by dehydration in an ethanol diluent serial, and 0.3% hydrogen peroxidase was used to inhibit the activity of endogenous peroxidase at room temperature for 30 min. Then, a microwave oven was adopted to perform antigen retrieval before the blocking of non-specific binding with 5% normal goat serum at 37 °C for 15 min. The overnight incubation of sections was performed with the primary antibody at 4 °C in a humidified box. After three washes with PBS, biotinylated anti-mouse immunoglobulin was adopted for the incubation of sections at 37 °C for 30 min. The visualization of samples was made using 3, 3-diaminobenzidine tetrahydrochloride, followed by counterstaining with hematoxylin. For the analysis, the positive percentages of ER stress-related proteins were explored in five random areas of every sample using Image J.
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4

Investigating Renal Endoplasmic Reticulum Stress

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Renal tissues were homogenized in RIPA buffer (P0013, Beyotime, Shanghai, China) supplemented with protease inhibitors (539134, EMD Biosciences Inc., San Diego, CA). After centrifugation (12,000 rpm/min) at 4 °C for 15 min, the supernatant was added to the loading buffer. Protein samples were processed for immunoblot analysis as previously reported (Dixon et al.). The following primary antibodies were used: β-actin (AP0060; Bioworld Technology), protein kinase -like endoplasmic reticulum kinase (PERK, ab65142; Abcam), activating transcription factor 6 (ATF6, ab203119; Abcam), IRE1α (CST3294), p-IRE1α (phosphorylation sites: S724; ab124945; Abcam), JNK (CST9252), p-JNK (phosphorylation sites: Thr183/Tyr185; CST4668), CCAAT-enhancer-binding protein-homologous protein (CHOP, ab179823; Abcam), 4-hydroxynonenal (4-HNE, ab46545; Abcam), glutathione peroxidase 4 (GPX4, ab125066; Abcam). The working concentration of β-actin used was 1:5000, and that of the other antibodies was 1:1000. Secondary antibodies were obtained from Dingguo Co. Ltd. (Beijing, China) and were used at the final dilution of 1:5000. The odesay software was used for analysis (Li Cor, Lincoln, NE).
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5

Immunohistochemical Analysis of Aortic Valve

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These aortic valve specimens were made into paraffin slides. After that, deparaffination and hydration were performed before the blocking procedure. Subsequently, these slides were incubated with primary antibodies separately, including ATF4 (Affinity; DF6008; 1:100 dilution), CHOP (Affinity; DF6025; 1:100 dilution), GRP78 (Proteintech; 11587-1-AP; 1:200 dilution), Runx2 (Abcam; ab23981; 1:200 dilution), ATF6 (Abcam; ab203119; 1:200 dilution), and XBP1 (Abcam; ab37152; 1:200 dilution). Nuclei were counterstained with hematoxylin. In the next stage, the positive staining was detected by an UltraSensitive SP IHC Kit and a DAB Kit (Maixin Biotech; KIT-9710; China).
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6

Protein Expression Analysis of Apoptosis and UPR Pathways

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The total protein was extracted by the modified RIPA buffer (P0013B; Beyotime, Shanghai, China), and the concentration was quantitated by the BCA protein assay kit (P0010; Beyotime, Shanghai, China). Then, the total protein was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Next, the proteins were transferred onto polyvinylidene fluoride (PVDF) membranes, and then the membranes were blocked in 5% skim milk diluted with TBST for 1 h at room temperature and probed with primary antibodies, including MFG-E8 (R&D Systems, AF2805, 1 : 500), BCL2 (Abcam, ab117115, 1 : 500), BAX (Abcam, ab216494, 1 : 500), cleaved caspase-3 (Abcam, ab90437, 1 : 500), GRP-78 (Abcam, ab230508, 1 : 500), XBP-1 (Abcam, ab230508, 1 : 500), ATF-6 (Abcam, ab203119, 1 : 500), ATF-4 (Abcam, ab23760, 1 : 500), CHOP (Abcam, ab23760, 1 : 500), p-PI3K (Abcam, ab125633, 1 : 500), PI3K (Abcam, ab154583, 1 : 500), p-AKT (Abcam, ab18785, 1 : 1000), AKT (Abcam, ab28422, 1 : 500), and β-actin (Abcam, ab209857, 1 : 1000) at 4°C overnight. Then, the membranes were incubated with a secondary rabbit anti-rabbit antibody (1 : 1000) the next day at room temperature for 1 h. The ImageJ software was employed for quantitation of the immunoreactive bands.
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7

Immunofluorescence Analysis of Apoptosis Markers

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After anesthetization, transcardial perfusion with 0.1M PBS was performed, followed by another perfusion with 4% paraformaldehyde (pH = 7.4). Then, the cerebral hemispheres were removed and put into 4% PFA for post-fixation (4°C, 24 h). Afterward, the brains were transferred to sucrose solution (30%, 2 days). Next, the brains were coronally sliced into 10 μm sections, which were then fixed on slides and used for immunofluorescence staining, and then blocked with 10% normal donkey serum for 2 h at room temperature and incubated at 4°C overnight with primary antibodies: ATF6 (1:200, abcam ab203119), caspase-3 (1:200, abcam ab49822), NeuN (1:500, abcam ab104224). Additionally, secondary antibodies were applied for 2 h at room temperature. Finally, the sections were assessed with a fluorescence microscope (Olympus, Tokyo, Japan) and pictures were further processed by Photoshop 13.0(Adobe Systems Inc., Seattle, WA, United States). Additionally, TUNEL (Roche Inc., Basel, Switzerland) staining was applied to assessed cellular apoptosis of brain tissues.
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8

Protein Expression Analysis in Liver Tissues

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Liver tissues or hepatocytes were lysed in a cold lysis buffer (Keygene) supplemented with phenylmethanesulfonyl fluoride (PMSF) at 4°C for 30 min. After separation by 12% sulfate‐polyacrylamide gel electrophoresis, the proteins were transferred to polyvinylidene difluoride membrane. The membrane was blocked at room temperature in phosphate‐buffered saline with Tween 20 buffer with 5% nonfat milk followed by incubation with primary antibody, including anti‐ERO1α (ab172954, Abcam), anti‐GRP78 (ab21685, Abcam), anti‐PERK (ab156919, Abcam), anti‐ATF6 (ab203119, Abcam), and anti‐XBP‐1 (ab37152, Abcam), anti‐DNMT1 (ab13537, Abcam), anti‐G9a (#3306, Cell Signaling Technology), anti‐H3K9me2 (ab176882, Abcam), anti‐H3 (ab1791, Abcam) at 4°C overnight. Blotting of β‐actin (bsm‐33036M, BIOSS) was used as a loading control. The membrane was washed three times and incubated with horseradish peroxidase‐conjugated secondary antibody (ZB‐2306, ZSGB‐BIO) for 2 h. After washing three times, the target proteins were detected using enhanced chemiluminescence solution (Beyotime Institute of Biotechnology), and the relative protein levels were determined by band densitometry using a gel imaging system (Bio‐Rad Laboratories, Inc.).
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9

Hepatic Protein Expression Analysis

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Ischemic hepatic lobes were dissected and homogenized in a buffer [2% SDS, 50 mM DTT, 62.5 mM Tris (pH 6.8), 10% glycerol] containing 1 mM PMSF (Amresco, LLC). The samples were then boiled for 5 min and centrifuged at 7,500 x g for 10 min at 4˚C. Supernatants were collected and protein concentrations were determined using a Bradford Protein Assay kit (Beyotime Institute of Biotechnology). Protein samples (35 µg) were then loaded and separated on a 12% SDS-PAGE. Following transfer onto a nitrocellulose membrane, the membranes were incubated with 5% skimmed milk to block non-specific antigens at room temperature for 2 h and probed with rabbit polyclonal antibodies (all 1:1,000) against ATF6 (cat. no. ab203119, Abcam), PERK (cat. no. ab65142, Abcam), glucose-regulated protein (GRP)78 (ab21685, Abcam), TNF-receptor-associated factor (TRAF)-2 (cat. no. ab62488, Abcam), C/EBP homologous protein (CHOP; cat. no. ab11419, Abcam), caspase-12 (cat. no. ab62463, Abcam) and GAPDH (cat. no. ab9485, Abcam) overnight at 4˚C. Following incubation with 1:1,000 diluted goat anti-rabbit IgG (H&L) secondary antibody (cat. no. G-21234, Themo Fisher Scientific) for 2 h at room temperature, the protein bands were developed using an enhanced chemiluminescence kit (Amersham; Cytiva).
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10

Comprehensive Immunoblotting Antibody Panel

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The following primary antibodies were used: mouse monoclonal antibodies against MHV N and S proteins (kind gifts of Dr Helmut Wege, University of Würzburg), rabbit polyclonal anti-SARS-CoV-2 spike glycoprotein antibody (ab272504, Abcam) mouse anti-GAPDH (IgM specific, G8795, Sigma-Aldrich), mouse anti-Flag (F3165, Sigma-Aldrich), rabbit anti-HA (3724, Cell Signaling Technology), rabbit anti-PERK (ab229912, Abcam), rabbit anti-HERPUD1 (ab150424, Abcam), rabbit anti-GRP78 (BIP, ab108613, Abcam), rabbit anti-eIF2α (9722, Cell Signaling Technology), rabbit anti-phospho-eIF2α (Ser51, 9721, Cell Signaling Technology), rabbit anti-ATF4 (10835-1-AP, Proteintech), rabbit anti-ATF6 (ab203119 and ab37149, Abcam), mouse anti-S6 (2317, Cell Signaling Technology) and rabbit RPL10a (ab174318, Abcam). Secondary antibodies used for western blotting were purchased from Licor: IRDye 800CW Donkey Anti-Mouse IgG (H+L), IRDye 800CW Donkey Anti-Rabbit IgG (H+L), IRDye 680RD Goat Anti-Mouse IgG (H+L) and IRDye 680RD Goat Anti-Mouse IgM (μ chain specific).
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