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19 protocols using anti atf4

1

Cellular stress response regulation assay

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24S-OHC [52 (link)] was dissolved in EtOH (Wako, Osaka, Japan). F12511 was the generous gift of Kowa (Aichi, Japan). Thapsigargin and CHX were purchased from Wako (Osaka, Japan). GSK2606414 and ISRIB were from Cayman Chemical (Ann Arbor, MI, USA). GCN2iB was from MedChemExpress (Monmouth Junction, NJ, USA). Thapsigargin, GSK2606414, CHX, and ISRIB were dissolved in dimethyl sulfoxide (DMSO; Wako). The following antibodies were from commercial sources: anti-PERK (Cat# 3192), anti-phospho-eIF2α (Cat# 3398), anti-eIF2α (Cat# 5324), and anti-GCN2 (Cat# 3302) were from Cell Signaling (Danvers, MA, USA); anti-β-actin (Cat# A5441) was from Sigma-Aldrich (St. Louis, MO, USA); anti-TIA1 (Cat# 12133-2-AP), anti-ATF4 (Cat# 10835-1-AP), and anti-TDP-43 (Cat# 12782-2-AP) were all from Proteintech (Chicago, IL, USA); anti-G3BP1 (Cat# 611126) was from BD Biosciences (Franklin Lakes, NJ, USA); anti-phospho-GCN2 (Cat# ab75836) was from Abcam (Cambridge, UK); and anti-puromycin (Cat# MABE343) was from Merck Millipore (Burlington, MA, USA); All other chemicals, of analytical grade, were obtained from Sigma-Aldrich or Wako.
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2

Antibody Reagents for Mitochondrial Protein Detection

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All reagents were purchased from Sigma‐Aldrich (St. Louis, MO, USA), Wako (Osaka, Japan), or Takara (Kyoto, Japan), unless otherwise stated. Anti‐DYKDDDDK antibody (Wako), anti‐TMEM160 antibody (Invitrogen, Carlsbad, CA, USA), anti‐VDAC1 antibody (Calbiochem‐Novabiochem, San Diego, CA, USA), anti‐HSPA9 (Sigma‐Aldrich), anti‐TOMM22 (Tom22) antibody [4 (link)], anti‐HSPD1 antibody (Sigma‐Aldrich), anti‐glyceraldehyde‐3‐phosphate dehydrogenase (anti‐GAPDH) antibody (Novus Biologicals, Littleton, CO, USA), anti‐LONP1 antibody (Sigma‐Aldrich), and Total OXPHOS Rodent WB Antibody Cocktail (Abcam, Cambridge, UK) containing anti‐ATP5A, UQCRC2, and MTCO1 antibodies were used to immunostain the cells and/or in immunoblot analysis. The anti‐TOMM40 (Tom40) and anti‐TOMM20 antibodies were obtained previously [5 (link), 6 (link)]. Anti‐ATF4, ATF5, and DDIT3 antibodies were purchased from Proteintech (Rosemont, IL, USA).
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3

Comprehensive Protein Expression Analysis

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Total ovary lysates were separated on SDS-PAGE. After electrophoresis, the protein was transferred to PVDF membrane. The membranes were blocked with 5% skimmed milk and incubated with anti-GRP78 (1:1000, #11587–1-AP, Proteintech, Hubei, China), anti-PARP1 (1:4000, #66520-1-lg, Proteintech), anti-PAR (1:1000, #4335-MC-100, Bio-techne, Minneapolis, USA), anti-mTOR (1:1000, #20657-1-AP, Proteintech), anti-p-mTOR (1:800, #sc-293133, Santa cruz, Dallas, Texas, USA), anti-KitL (1:1000, #bs-0545R, Biorbyt, Hubei, China), anti-p-IRE1α (1:800#, bs-16698R, Biorbyt), anti-IRE1α (1:1000, #27528-1-AP, Proteintech), anti-ATF4 (1:1000, #10835-1-AP, Proteintech), anti-p-PERK (1:800, #Orb336657, Biorbyt), anti-PERK (1:1000, #24390-1-AP, Proteintech), anti-HA-tag (1:1000, #30701ES60, YEASEN), anti-FLAG-tag (1:1000, #30501ES60, YEASEN) and anti-GAPDH (1:4000, #ab8245, Abcam, Cambridge, UK) antibodies overnight at 4 °C. After TBST washing, the membranes were treated with the corresponding peroxidase-conjugated secondary antibody, and then the signal was detected with an Enhanced Chemiluminescence Detection Kit (#32106, Thermo Scientific, Waltham, MA, USA) on Tanon 4500 gel imaging system (Shanghai, China).
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4

Comprehensive Protein Expression Analysis

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Total ovary lysates were separated on SDS-PAGE. After electrophoresis, the protein was transferred to PVDF membrane. The membranes were blocked with 5% skimmed milk and incubated with anti-GRP78 (1:1000, #11587–1-AP, Proteintech, Hubei, China), anti-PARP1 (1:4000, #66520-1-lg, Proteintech), anti-PAR (1:1000, #4335-MC-100, Bio-techne, Minneapolis, USA), anti-mTOR (1:1000, #20657-1-AP, Proteintech), anti-p-mTOR (1:800, #sc-293133, Santa cruz, Dallas, Texas, USA), anti-KitL (1:1000, #bs-0545R, Biorbyt, Hubei, China), anti-p-IRE1α (1:800#, bs-16698R, Biorbyt), anti-IRE1α (1:1000, #27528-1-AP, Proteintech), anti-ATF4 (1:1000, #10835-1-AP, Proteintech), anti-p-PERK (1:800, #Orb336657, Biorbyt), anti-PERK (1:1000, #24390-1-AP, Proteintech), anti-HA-tag (1:1000, #30701ES60, YEASEN), anti-FLAG-tag (1:1000, #30501ES60, YEASEN) and anti-GAPDH (1:4000, #ab8245, Abcam, Cambridge, UK) antibodies overnight at 4 °C. After TBST washing, the membranes were treated with the corresponding peroxidase-conjugated secondary antibody, and then the signal was detected with an Enhanced Chemiluminescence Detection Kit (#32106, Thermo Scientific, Waltham, MA, USA) on Tanon 4500 gel imaging system (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

Western Blot Analysis of UPR Markers

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Rat Müller cells were washed with PBS and lysed with RIPA lysis buffer (Beyotime, China) on ice for 30 minutes. The protein concentrations were detected by the BCA protein assay (Beyotime). The proteins were separated in 4–6% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE, Beyotime, China) and then transferred to a PVDF membrane (Beyotime). After blocking with 5% nonfat milk in TBST buffer (200 mM Tris and 1.5 M NaCl with 0.1% Tween 20), the membranes were blotted at 4°C overnight with the following primary antibodies: anti-XBP1s (1 : 600; Proteintech), anti-GRP78 (1 : 800; Proteintech), anti-VEGF (1 : 600; Proteintech); anti-ATF4 (1 : 800; Proteintech), and anti-ATF6 (1 : 200; Proteintech). The membranes were sequentially probed with horseradish peroxidase-conjugated goat anti-rabbit antibody (Boster Biological Technology) at room temperature for 2 hours. β-Actin was served as the loading control. Enhanced chemiluminescence (ECL, Beyotime) was used for imaging, and finally, the optical density of the band was analyzed by GeneTools software (Syngene, Synoptic Ltd. USA). All experiments were repeated for 3 times independently.
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7

6-OHDA-Induced Dopaminergic Neurotoxicity

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Stock solutions of 6-hydroxydopamine (6-OHDA; Tocris), guanabenz acetate salt, clonidine, efaroxan (Sigma) were prepared in ddH2O; camptothecin (CPT; Tocris) was prepared in DMSO. The following antibodies were used: anti-ATF4 was commercially generated for our laboratory (Liu et al., 2014 (link); Pasini et al., 2015 (link)); anti-GADD34 was from Proteintech; anti-tyrosine hydroxylase (TH) was from EMD Millipore; anti-ERK was from Santa Cruz Biotechnology; anti-parkin (PARK8), anti-phospho-eIF2α (S51) and total eIF-2α were from Cell Signaling Technology.
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8

Comprehensive Protein Expression Analysis

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Total ovary lysates were separated on SDS-PAGE. After electrophoresis, the protein was transferred to PVDF membrane. The membranes were blocked with 5% skimmed milk and incubated with anti-GRP78 (1:1000, #11587–1-AP, Proteintech, Hubei, China), anti-PARP1 (1:4000, #66520-1-lg, Proteintech), anti-PAR (1:1000, #4335-MC-100, Bio-techne, Minneapolis, USA), anti-mTOR (1:1000, #20657-1-AP, Proteintech), anti-p-mTOR (1:800, #sc-293133, Santa cruz, Dallas, Texas, USA), anti-KitL (1:1000, #bs-0545R, Biorbyt, Hubei, China), anti-p-IRE1α (1:800#, bs-16698R, Biorbyt), anti-IRE1α (1:1000, #27528-1-AP, Proteintech), anti-ATF4 (1:1000, #10835-1-AP, Proteintech), anti-p-PERK (1:800, #Orb336657, Biorbyt), anti-PERK (1:1000, #24390-1-AP, Proteintech), anti-HA-tag (1:1000, #30701ES60, YEASEN), anti-FLAG-tag (1:1000, #30501ES60, YEASEN) and anti-GAPDH (1:4000, #ab8245, Abcam, Cambridge, UK) antibodies overnight at 4 °C. After TBST washing, the membranes were treated with the corresponding peroxidase-conjugated secondary antibody, and then the signal was detected with an Enhanced Chemiluminescence Detection Kit (#32106, Thermo Scientific, Waltham, MA, USA) on Tanon 4500 gel imaging system (Shanghai, China).
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9

Western Blot Analysis of Apoptosis Markers

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Following SDS‒PAGE using Bis–Tris 10% gels (Thermo Fisher Scientific, MA, USA), proteins were directly blotted onto PVDF membranes. Subsequently, the membranes were blocked with RotiBlock (Roth, Germany) and incubated with the following antibodies: anti-ABCC2 (12559; CST, Danvers, MA, USA), anti-ABCG2 (42078; CST, Danvers, MA, USA), anti-ATF4 (10835; Proteintech), anti-ATF6 (15794; Proteintech), anti-BIM (2933; CST, Danvers, MA, USA), anti-BiP (Grp78; 610978; BD Biosciences), anti-cleaved caspase-3, -7, -9, (9644; 8438; 7237; all CST, Danvers, MA, USA) anti-CHOP (Gadd 153; sc-793; Santa Cruz, USA), anti-phospho-IRE1α (phospho S724; ab124945; abcam), anti-LC3B (3868; CST, Danvers, MA, USA), anti-MCL-1 (4572; CST, Danvers, MA, USA) anti-PDI (610946; BD Biosciences), anti-NOXA (OP180; Calbiochem), anti-polyUb (PW 8805-0500; Enzo, NY, USA), and anti-GAPDH (hrp-60004; Proteintech).
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10

Immunofluorescence Analysis of Müller Cells

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Rat Müller cells cultured on a 6-well chamber were washed twice with PBS and fixed with 4% paraformaldehyde in PBS for 10 min, followed by penetration with Triton X-100 (0.1%, Invitrogen) for 15 minutes. The cells were blocked with 5% BSA (Invitrogen) in PBS for 1 hour and incubated with primary antibodies at 4°C overnight. The cells were then incubated with secondary antibodies (1 : 200; Cy3-labled goat anti-rabbit IgG, Boster Biological Technology, Wuhan, China) at room temperature for 60 minutes. After washing with PBS three times (2 min/time) and staining with DAPI to visualize nuclei, the cells were analyzed under a fluorescence microscope (Olympus, Japan). Primary antibodies used rabbit anti-mouse glial fibrillary acidic protein (GFAP, Thermo Fisher Scientific), anti-XBP1s (1 : 600, Proteintech, USA), anti-ATF4 (1 : 800, Proteintech), and anti-ATF6 (1 : 200, Proteintech).
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