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9 protocols using ab32371

1

Probing Apoptosis Regulators via Western Blotting and Immunoprecipitation

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For western blotting, proteins were obtained using Tris-lysis buffer containing 1% TritonX. Western blotting was performed using the following antibodies: mouse anti-BCL-2 (M088701-2, Dako Agilent, Hamburg, Germany), rabbit anti-BCL-XL (2762S, Cell Signaling, Beverly, MA, USA), rabbit anti-MCL-1 (ADI-AAP-240F, Enzo, Farmindale, NY, USA), rabbit anti-BIM (3183S, Cell Signaling), mouse anti-NOXA (ALX-804-408, Enzo), rabbit anti-BAK (06-536, Upstate/Merck), mouse anti-BAX (2772S, Cell Signaling) and mouse anti-GAPDH (5G4-6C5, BioTrend, Hy Test Ltd., Turku, Finland). Immunoprecipitation was performed using the following antibodies: hamster anti-BCL-2 (551051, BD Bioscience, Heidelberg, Germany), rabbit anti-BCL-XL (ab32370, Abcam), rabbit anti-MCL-1 (ADI-AAP-240F, Enzo), mouse anti-BAX (610983, BD Bioscience), and rabbit anti-BAK (ab32371, Abcam). Antibodies were crosslinked to protein G dynabeads (Invitrogen, Karlsruhe, Germany). CHAPS containing lysates were incubated overnight at 4°C with the antibody-protein G complexes before the precipitates were washed in lysis buffer and analyzed by western blotting.
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2

Cellular Signaling Pathways Modulation

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RPMI 1640 medium (61870-036) and fetal bovine serum [FBS] (10099141) were purchased from Gibco (USA, NY). CORT and neferine (HY-N0441) were purchased from MedChem Express (NJ, USA). The GenElute Gel Extraction Kit (NA1111) was purchased from Sigma-Aldrich (Darmstadt, Germany). BamHI (R0136S) and XhoI (R0146S) were purchased from NEB (NY, USA). Lipofectamine 3000 Transfection Reagent (L3000015) was purchased from Invitrogen (CA, USA). G418 (G8161) was purchased from Solarbio (Beijing, China). RNApure Tissue and Cell Kit (CW0584), HiFiScript cDNA Synthesis Kit (CW2569), and Super TaqMan Mixture (CW2698) were obtained from Cwbiotech (Beijing, China). Antibodies against Bcl-2 (ab32124), Bax (ab32503), Bad (ab32445), p53 (ab26), Bak (ab32371), succinate-CoA ligase GDP-forming beta subunit [SUCLG2] (ab96172), aconitase 2 [ACO2] (ab110321), malate dehydrogenase 1 [MDH1] (ab180152), citrate synthase [CS] (ab96600), isocitrate dehydrogenase [IDH] (ab172964), NF-κB p65 (ab16502), and glyceraldehyde 3-phosphate dehydrogenase [GAPDH] (ab8245) were purchased from Abcam (Massachusetts, US). ELISA kits for IL-1β (ab100562), IL-2 (ab174444), IL-6 (ab46027), TNF-α (ab181421), interferon-γ [IFN-γ] (ab46025), and granulocyte colony-stimulating factor [G-CSF] (ab100524) were purchased from Abcam. Rabbit and mouse secondary antibodies were purchased from ECL.
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3

CRISPR-Mediated Knockout and Rescue of Apoptosis Regulators

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LentiCRISPR v2-derived constructs (Addgene #52961) encoding sgRNA targeted BAK, BAX or BOK and Cas9 were cotransfected with psPAX2 (Addgene #12260) and pMD2.G (Addgene #12259) into 293 T cells at a 10:7:5 (a total of 16 μg plasmids) ratio on a 10 cm plate with polyethyleneimine. The supernatant of the culture medium was collected 48 h post transfection and filtered through a 0.45 μm filter. H292 cells were transducted with lentivirus in the presence of 6 μg/ml polybrene (Santa Cruz Bio., Texas, USA) for 12 h. Three days after transduction, cells were diluted into single cell per well and were selected with 2 μg/ml puromycin (Sigma–Aldrich, St. Louis, Missouri, USA). Knockout status of expanded single-cell clones was validated by gene sequences and WB analysis of immunoblotting with BAK antibody (1:1000, #ab32371, Abcam, Cambridge, England), BAX antibody (1:1000, #2772 s, CST, USA) or BOK antibody (1:1000, #ab233072, Abcam, Cambridge, England). The rescue expression of BOK followed Xu et al. [22 (link)]. The sgRNA sequences for CRISPR/Cas 9 knockout were listed in Supplementary Table 1.
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4

Western Blot Analysis of Apoptotic and Proliferative Markers in MDA-MB-468 Cells

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The treated MDA-MB-468 cells were lysed with the cell lysis buffer. Protein concentration was measure by the BCA Protein Assay kit (Beyotime Biotechnolgy, Beijing). Lysates were separated in 10% SDS-PAGE and then transferred onto the nitrocellulose membrane (Millopore, USA). The membrane was blocked with 5% skimmed milk in TBST buffer at room temperature for 1 h. After that, the membranes were incubated with anti-Caspase 3 (1:5000, ab32351, Abcam, Cambridge, MA, USA), anti-Cleaved Caspase 3 (1:500, ab32042, Abcam), anti-Ki67 (1:5000, ab92742, Abcam), anti-PCNA (1:2000, ab92552, Abcam), anti-Bak (1:10000, ab32371, Abcam), anti-Bax (1:1000; ab32503, Abcam), anti-Bcl-2 (1:1000, ab32124, Abcam), anti-apaf-1 (1:1000, ab2001, Abcam), anti-Cytochrome c (1:5000; ab133504, Abcam), anti-Akt (1:1000; #4685, Cell Signaling Technology, Danvers, MA), anti-phosphorylated-Akt (1:1000, #4060 CST), anti-p38 (1:1000, #8690, CST), anti-phosphorylated p38 (1:1000, #4511, CST), anti-NF-κB (1:1000, #8242, CST), anti-p21 (1:1000; ab109520, Abcam), anti-p27 (1:5000; ab32034, Abcam) and GAPDH (1:2500, ab9485, Abcam) at 4°C overnight and then secondary antibodies (1:5000) were incubated for 1 h at room temperature. The proteins were visualized by using the enhanced chemiluminescence reagent (Bio-Rad, USA).
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5

Protein Expression Analysis in Cells

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Total proteins were isolated from cells using RIPA lysis buffer. After loading 25 μg cellular protein samples on SDS‐PAGE gels, proteins of the same weight from each group were separated and transferred to PVDF membranes. Subsequently, membranes were blocked with 5% skimmed milk for 1 h at room temperature and later incubated with primary antibodies overnight at 4°C. The main antibodies include rabbit anti‐human CD1E antibody (1: 1000, ab187157, Abcam), rabbit anti‐human STK11 antibody (1: 1000, ab138386, Abcam), rabbit anti‐human Bax antibody (1: 1000, ab32503, Abcam), rabbit anti‐human Bak antibody (1: 10000, ab32371, Abcam), rabbit anti‐human Bcl‐2 antibody (1: 1000, ab32124, Abcam), rabbit anti‐human AMPK antibody (1: 1000, ab207442, Abcam), rabbit anti‐human p‐AMPK antibody (1: 1000, ab133448, Abcam), and rabbit anti‐human β‐actin antibody (ab115777, Abcam). Following incubation with primary antibodies, they were incubated with secondary antibody IgG (1: 2000, ab97051, Abcam) for 1 h at room temperature. Protein bands were detected with enhanced chemiluminescence reagents (Merck Millipore). β‐actin was used as an internal reference.
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6

Silencing EPO in ARPE-19 Cells

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siRNA Transfection:
ARPE-19 cells were
seeded in 24-well plates at a density of 6 × 104 cells/well
with DMEM (0.1 mL) containing FBS (10%) and streptomycin/penicillin
(1%). ARPE-19 cells were treated with 175 ng (final concentration
of 23 nM) of siRNA against EPO (Sigma, sense = 5′GACCCUUCAGCUUCAUAUATT,
antisense = 5′UAUAUGAAGCUGAAGGGUCTT) and random sequence control
siRNA (Allstars control negative siRNA, Qiagen, Valencia, CA) in 100
μL of culture medium without serum. Transfection was conducted
with HiPerFect transfection reagent (Qiagen, Valencia, CA), and cells
were harvested 48 h post-transfection. Proteins were assayed by western
blot for detection of EPO (ab226956, Abcam; sc5290, Santa Cruz), AIF
(EMD Millipore), BCL-xL (sc-634, Santa Cruz Biotechnology), caspase-3
(EMD Millipore), BAK (ab32371, Abcam), and actin (sc-47778, Santa
Cruz Biotechnology). Protein localization and expressions were also
analyzed by immunocytochemistry.
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7

Investigating SHP2 Inhibition and Bortezomib Effects

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SHP099 (HY-100388A) and bortezomib (HY-10227) were purchased from MedChemExpress (Princeton, NJ, United States). RMC-4550 (S8718) was obtained from Selleckchem (Houston, TX, United States). The primary antibodies against SHP2 (#3397), phospho-SHP-2 (Tyr542) (#3751), and P21 (#2947) were obtained from Cell Signaling Technology. Anti-GAPDH (10494-1-AP) was purchased from Proteintech. The primary antibodies against ERK (AF1051) and phospho-ERK (AF1891) were procured from Beyotime Biotechnology. The antibodies specific for BAK (ab32371) and cleaved caspase-3 (ab32042) were obtained from Abcam. HRP-conjugated secondary antibodies were purchased from Servicebio.
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8

Western Blot Analysis of Immune Proteins

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The whole cell lysates (Beyotime, Shanghai, China) were used to harvest total protein. The equal amount of protein extract was then separated by SDS-PAGE and transferred electrophoretically to polyvinylidene difluoride membrane. Subsequently, membranes were blocked in 5% non-fat dry milk. The membranes were incubated with the appropriate dilutions of primary antibodies against NOD1 antibody (1:1000, ab217798, Abcam, Cambridge, MA, US), BAK1 (1:1000, ab32371, Abcam, Cambridge, MA, US), NLRP6 (1:1000, ab58705, Abcam, Cambridge, MA, US), and GAPDH (1;1500; Abcam, Cambridge, MA, USA) antibody sampler kit (9782 T) at 4 °C. The more detailed steps have been illustrated as previously described [24 (link)].
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9

Apoptosis-Related Protein Immunoblotting

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Cell lysates (10 μg) were resolved on 4%−20% SDS-polyacrylamide gels, electrotransferred onto nitrocellulose membranes, and blocked for 1 hour at 25°C in 5% nonfat dry milk / 0.1% Tween. Blots were incubated with antibodies at 4°C overnight, washed in 0.05% Tween, and incubated with horseradish peroxidase-conjugated secondary antibodies for 1 hour. The blots were washed and immunocomplexes were detected using SuperSignal West Femto (Thermo #34095). Antibodies: Bak (ab32371, Abcam), Bax (ab32503, Abcam), Bcl-2 (sc-492, Santa Cruz), Bcl-xl (sc8392, Santa Cruz), and Mcl-1 (sc819, Santa Cruz).
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