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22 protocols using ab184909

1

Western Blot Analysis of Cellular Proteins

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Proteins were extracted from tissues or cells in RIPA assay and protein concentration was determined by a BCA protein assays kit (Thermo Scientific). Protein were separated into 10% SDS‐PAGE and transferred to polyvinylidene difluoride (PVDF) membranes (Millipore Corp.). The PVDF membranes were incubated by ORMDL3 (ab211522, 1:1000, Abcam), p‐PERK (3179, 1:1000, Cell Signaling Technology, Inc.), PERK (5683, 1:1000, Cell Signaling Technology, Inc.), p‐eiF2α (ab32157, 1:1000, Abcam), eiF2α (ab169528, 1:1000, Abcam), ATF4 (ab184909, 1:1000, Abcam), HSPA5 (ab21685, 1:1000, Abcam), GPX4 (ab125066, 1:1000, Abcam) and β‐actin (ab8226, 1:10000, Abcam) at 4°C overnight. PVDF membranes were incubated with horseradish peroxidase‐conjugated secondary antibodies (A0208, A0216, Beyotime, 1:5000) for 2 h. The signal was tested with the chemiluminescence system (Amersham Pharmacia).
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2

Cellular ROS Assay and Ferroptosis Markers

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DCFDA/H2DCFDA-Cellular ROS Assay Kit was provided by Abcam (ab113851, Cambridge, MA, USA). Erastin (HY-15763, ferroptosis inducer) was purchased from MedChemExpress (Shanghai, China). The following primary antibodies were used in this study: anti-ATF-4 antibody (ab184909, Abcam, USA), anti-CHAC1 antibody (MA5-26311, Invitrogen, Carlsbad, CA, USA), anti-GPX4 antibody (ab125066, Abcam, USA), anti-transferrin receptor antibody (ab277635, Abcam, USA), anti-ferritin antibody (ab75973, Abcam, USA), anti-Hsp70 antibody (ab2787), and anti-GAPDH antibody (ab8245, Abcam, USA). Goat anti-mouse IgG (HRP) (ab6789, Abcam, USA) and goat anti-rat IgG (HRP) (ab97057, Abcam, USA) were used as secondary antibody for Western blotting.
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3

Immunostaining of ATF4 in Fibroblasts

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Fibroblast lines were plated on eight-well chamber slides and grown in FGM overnight; cells were then dosed with SAL (2.5 μM) or ISRIB (12.5 nM) or vehicle control for 3 days. Cells were then washed in PBS and fixed in 4% paraformaldehyde in PBS for 15 minutes. They were then permeabilized in 0.1% Triton X-100 in phosphate-buffered saline for 5 minutes. Slides were blocked in 3% FBS, 2% normal goat serum in PBS for 1 hour. ATF4 antibody (ab184909; Abcam) was diluted in blocking buffer 1:200 and incubated overnight at 4°C. After washing 3 × 15 minutes in PBS, secondary antibody (A-11034; Thermo Fisher) was diluted 1:500 in blocking buffer and incubated for 1 hour at room temperature. F-actin was visualized with Phalloidin, DyLight 650, (21838; Thermo Fisher) diluted 1:200 in blocking buffer was incubated for 15 minutes. Nuclei were visualized with 4′,6-diamidino-2-phenylindole (DAPI). Images (×10) were obtained on a Zeiss Axio Imager A2 (Zeiss GMBH, Oberkochen, Germany) utilizing Axiovision software. High-magnification images were obtained on a Zeiss 510 Meta confocal microscope with a ×63 objective utilizing Zen software.
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4

Redox-Sensitive Protein Regulation Protocol

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The chemical (2S, 3S)-1,4-Bis-sulfanylbutane-2,3-diol (DTT, CAS No. 3483-12-3) was obtained from Sigma; it is a strong reductant with the chemical formula C4H10O2S2 and MW of 154.25 g/mol. Its reducibility is largely due to the conformational stability after oxidation (containing disulfide bond). In this experiment, 3.09 g DTT powder was completely dissolved in 20 mL 0.01 M sodium acetate to obtain 1 M DTT stock solution, which was packed and stored at −20 °C before use.
Specific antibody against Nrf1 was made in our own laboratory [25 (link)]. All nine distinct antibodies against Nrf2 (ab62352), GCLC (ab207777), GCLM (ab126704), HO-1 (ab52947), GPX1 (ab108427), XBP1 (AB109221), ATF4 (ab184909), ATF6 (ab227830) and P4HB (ab137180) were obtained from Abcam (Cambridge, UK). The first three antibodies against TALDO (D623398), GSR (D220726) and NQO1 (D26104) were purchased from Sangon Biotech (Shanghai, China). The second three antibodies against BIP (bs-1219R), Chop (bs-20669R) and pIRE1 (bs-16698R) were from Bioss (Beijing, China). The third three antibodies against PSMB5 (A1975), PSMB6 (A4054), PSMB7 (A14771) were from ABclonal (Wuhan, China). Lastly, three antibodies to p-eIF2α (#5199) were from Cell Signaling Technology (Boston, MA, USA), p-PERK (sc-32577) from Santa CruZ (Santacruz, CA, USA), and β-actin (TA-09) from ZSGB-BIO (Beijing, China), respectively.
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5

Evaluation of Ferroptosis Markers in Cells

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Brucine, ferric ammonium citrate (FAC), and glutathione (GSH) were all purchased from Sigma-Aldrich (Saint Louis, MO, USA). Ferrostatin-1 (Fer-1), liproxastin-1, and 4-phenylbutyrate (4-PBA) were all obtained from Selleck Chemicals (Houston, TX, USA). Primary antibodies against GRP78 (ab12685), ATF3 (ab254268), ATF4 (ab184909), GPX4 (ab125066), cystine-glutamate antiporter xCT (ab175186), ferritin light chain (ab69090), ferritin heavy chain (ab75972), FPN (ab78066), TF (ab82411), TFR (ab1086), ATG5 (ab108327), LC3B (ab192890), p62 (ab109012), Beclin-1 (ab207612), superoxide dismutase 1 (SOD1) (ab51254), and catalase (ab209211) were all from Abcam (Cambridge, UK). Anti-PERK (#5683) and anti-β-Actin (#4970) antibodies were from Cell Signaling Technology (Beverly, MA, USA). The other reagents were purchased from Sigma-Aldrich.
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6

Protein Expression Analysis in Hepatocytes

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The treated human LO-2 hepatocytes were lysed to isolate proteins, which were subsequently loaded and separated with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Then, the proteins were transferred onto the polyvinylidene difluoride (PVDF) membrane and incubated with 5% nonfat milk. The membrane was then incubated with primary antibody against NOX-4 (1:1000, ab133303, Abcam), NLRP3 (1:1000, ab263899, Abcam), p-eIF-2α (1:1000, ab169528, Abcam), ATF4 (1:1000, ab184909, Abcam), GADD34 (1:1000, ab236516, Abcam), CHOP (1:1000, ab11419, Abcam), NF-κB p65 (1:1000, ab288751, Abcam) or β-actin (1:1000, ab8226, Abcam), which was further incubated with an HRP-conjugated secondary antibody. Finally, the blots were developed with electrochemiluminescence (ECL) reagents and analyzed using Image J software [25 (link)].
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7

UPR Pathway Protein Analysis

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Cells were harvested and lysed in LDS sample buffer (Invitrogen) at 5×106 cells/mL, separated electrophoretically using Bolt 4–12% Bis-Tris plus gels (Invitrogen), and transferred onto PVDF membranes (0.2 μm pore size) using PVDF Mini Stacks and iBlot 2 (Invitrogen). Membranes were probed with rabbit antibodies against KDSR (ab153960, Abcam; 1:1000), PERK (5683T, Cell Signaling Technology; 1:1000), ATF4 (ab184909, Abcam; 1:1000), ATF6 (65880T, Cell Signaling Technology; 1:1000), IRE1α (3294T, Cell Signaling Technology; 1:1000), and histone H3 (ab1791, Abcam; 1:1000) at 4°C overnight. After washing, the membranes were incubated with HRP-linked goat anti-rabbit IgG antibody (31460, Invitrogen; 1: 200,000) at room temperature for 1 hour. Chemiluminescent signals were developed using the SuperSignal West Femto Substrate (ThermoFisher) and detected using a ChemiDoc imaging system (Bio-Rad).
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8

Western Blot Analysis of Stress Response

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Cells were lysed in radioimmunoprecipitation assay buffer buffer including protease and phosphatase inhibitors; protein was run on a 10% SDS Tris-glycine gel according to standard practices. After transfer to polyvinylidene difluoride membrane, membranes were blocked with 5% nonfat dry milk (Blotto) in PBS and then incubated in blocking buffer + 0.1% Tween 20 overnight with antibodies: ATF4 (ab184909, 1:1000; Abcam), Phospho S51 eIF2α (ab32157, 1:800; Abcam), eIF2α (9722, 1:100; Cell Signaling Technologies, Danvers, MA, USA), CRP55 (ab92516; 1:2000; Abcam). Detection was carried out using HRP labeled antibodies and ECL.
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9

UPR Pathway Protein Analysis

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Cells were harvested and lysed in LDS sample buffer (Invitrogen) at 5×106 cells/mL, separated electrophoretically using Bolt 4–12% Bis-Tris plus gels (Invitrogen), and transferred onto PVDF membranes (0.2 μm pore size) using PVDF Mini Stacks and iBlot 2 (Invitrogen). Membranes were probed with rabbit antibodies against KDSR (ab153960, Abcam; 1:1000), PERK (5683T, Cell Signaling Technology; 1:1000), ATF4 (ab184909, Abcam; 1:1000), ATF6 (65880T, Cell Signaling Technology; 1:1000), IRE1α (3294T, Cell Signaling Technology; 1:1000), and histone H3 (ab1791, Abcam; 1:1000) at 4°C overnight. After washing, the membranes were incubated with HRP-linked goat anti-rabbit IgG antibody (31460, Invitrogen; 1: 200,000) at room temperature for 1 hour. Chemiluminescent signals were developed using the SuperSignal West Femto Substrate (ThermoFisher) and detected using a ChemiDoc imaging system (Bio-Rad).
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10

Quantifying ER Stress Markers in Cells

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ER-related markers, including heat shock protein family A (Hsp70) member 5 (HSPA5, also known as GRP78), DNA Damage Inducible Transcript 3 (DDIT3, also known as CHOP), activating transcription factor 4 (ATF4) and caspase12 (CASP12), were quantified by western blot. The primary antibodies were purchased from Abcam, including anti-HSPA5 (ab21685; Abcam, Cambridge, MA, USA), anti-DDIT3 (ab11419; Abcam), anti-ATF4 (ab184909; Abcam), anti-CASP12 (anti-caspase12; ab62484; Abcam), anti-PDE4A (ab200383; Abcam). Total protein was extracted using RIPA lysis buffer (Beyotime) and quantified by BCA kit (Beyotime). Protein was separated and transferred onto PVDF membranes. Protein on membranes was blocked by 5% skim milk and subsequently incubated with the primary antibodies and the secondary antibody (ab205718; Abcam). Finally, the protein bands were emerged using the ECL reagent (Beyotime) and imaged using Amersham Imager. A total of 3 independent experiments were implemented.
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