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27 protocols using dykddddk tag

1

TLT2-mediated IL-6 Signaling Regulation

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The following reagents were used in this study. Middlebrook 7H10 agar and Middlebrook 7H9 broth medium were purchased from BD Difco Laboratories (Sparks, MD, United States). Antibodies (Abs) against STAT3, p-STAT3 (Y705), HA tag, and DYKDDDDK tag were obtained from Cell Signaling Technology. Antibody against β-actin was obtained from Sigma-Aldrich. An inhibitor of STAT3 (Stattic) was obtained from Selleck. Recombinant human TLT2 Fc chimera and recombinant human IgG1 Fc were obtained from R&D Systems. LeafTM purified anti-human IL-6 antibody, purified anti-human CD126 (IL-6Rα) antibody, and IgG1 were obtained from BioLegend. Recombinant human IL-6 (Catalog 200-06) were obtained from PeproTech. Recombinant mouse TLT2 (Catalog CM67) were obtained from Novoprotein.
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2

Murine Cytokine Signaling Pathway Assay

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Murine recombinant tumor necrosis factor-α (TNF-α) (#575204) and interleukin-1β (IL-1β) (#575102) were purchased from Biolegend. GSK126 was obtained from MedChemExpress. SB 203580 and PD98059 were purchased from AdooQ Bioscience.
The following primary antibodies were used : Lamin A/C (#2032), GAPDH (#2118), β-Actin (#4967), p65 (#6956), phospho-p65 (Ser536) (#3033), IKKβ (#2678), p53 (Rodent Specific) (#32532), phospho-p53 (Ser15) (#9284), IκBα (#4812), phospho-IκBα (#2859), NF-κB1 p105/p50 (#13586), NF-κB2 p100/p52 (#4882), phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (#4370), phospho-p38 MAPK (Thr180/Tyr182) (#4511), phospho-SAPK/JNK (Thr183/Tyr185) (#4668), DYKDDDDK Tag (#2368), phospho-histone H2A.X (Ser139) (#9718), and acetyl-p53 (Lys379) (#2570), CDK6 (#3136), Ezh2 (#5246), RelB (#4922), all purchased from Cell Signaling Technology, and p21 (#sc-6246), which was purchased from Santa Cruz. Phospho-p53 (Ser20) (# PA5–104741), phospho-p53 (Ser37) (#HY-P80843) and phospho-RelA/p65 (Ser276) (#NB100–82086) antibodies were purchased from Invitrogen, MedChemExpress and Novus Biologicals, respectively.
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3

Antibody Optimization for Western Blot, IHC, and IF

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The following antibodies were purchased from Cell Signaling and used at the indicated dilution for western blot analysis, immunohistochemistry, and immunofluorescence: pan-TEAD (13295, 1:1000), p38 MAPK (8690, 1:1000), phospho-p38 MAPK (4511, 1:1000), YAP (14074, 1:1000), TAZ (4883, 1:1000), Lats1 (3477, 1:1000), p-MK2 (3007, 1:1000), p-ERK (4370, 1:1000), DYKDDDDK tag (2368, 1:1000), Myc tag (2276, 1:1000), p38α (2371, 1:1000), p38β (2339, 1:1000), p38γ (2307, 1:1000), and p38δ (2308, 1:1000). The following antibodies were purchased from Santa Cruz Biotechnology and used at the indicated dilution for western blot analysis and immunofluorescence: YAP (sc-101199, 1:1000), HA (sc-7392, 1:5000), Myc (sc-40, 1:5000), GAPDH (sc-25778, 1:1000). TEAD4 (ab58310, 1:1000) was purchased from Abcam, Flag (A8592, 1:10,000) and vinculin (V9131, 1:5000) was purchased from Sigma, TEAD1 (610923, 1:1000) was purchased from BD Biosciences, Lats2 (A300-479A, 1:1000) was purchased from Bethyl Laboratories, and NFAT5 (bs-9473R OWL 1:1000) was purchased from One World Lab.
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4

Immunoblotting Analysis of Liver Proteins

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Liver and cellular lysates were obtained by centrifugation as previously described (Kim et al., 2016 ). Immunoblots were conducted on 3–5 samples randomly chosen within each experimental cohort with antibodies against Nicastrin (#5665), Presenilin 1 (#5643), Presenilin 2 (#9979), DYKDDDDK-tag (#14793), and β-actin (#4970) from Cell Signaling; mouse ApoC3 from Ionis; human ApoC3 (33A-R1a) from Academy Biomedical; human ApoB (MAB4124) and PCSK9 (AF3985) from R&D systems; ApoB (ab20737), LDLR (ab30532), Syndecan-1 (ab128936) from Abcam; and GFP (sc-9996) from Santa Cruz.
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5

Immunofluorescence Staining of Adherent Cells

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Cells seeded onto cover slips in 6-well plates were fixed in 4% paraformaldehyde solution for 10 min with gentle rocking. Fixed cells were washed three times in PBS, incubated in blocking buffer (PBS/2% BSA/0.2% Triton X-100) for 20 min and incubated with primary antibody diluted in blocking buffer at 4°C overnight. The following primary antibodies were used: E-cadherin (3195: Cell Signaling), V5 (R96025; ThermoFisher), SBP tag (SB19-C4; Santa Cruz), GM130 (ab31561; Abcam), DYKDDDDK Tag (14793: Cell Signaling), BBF2H7/CREB3L2 (MABE1018: Millipore). Following primary antibody incubation, cells were washed three times in PBS and incubated with Alexa Fluor 488- or 568-conjugated secondary antibody (Life Technologies) diluted in blocking buffer for 1 h, followed by three PBS washes and mounting of slides using DAPI Fluoromount G (Southern Biotech). For Phallodin immunofluorescence, rhodamine phallodin was diluted in blocking buffer and incubated at 4°C overnight, cells were then washed three times in PBS and mounted. Images were taken using an Olympus FV10i LIV laser scanning confocal microscope.
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6

Protein Expression Profiling in GSC and GBM

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Protein was extracted from GSC cells or GBM cells. Primary antibodies to the following were used: GAPDH (Cell Signaling Technology, 5174), β-actin (Cell Signaling Technology, 14074), N-cadherin (Cell Signaling Technology, 13116), E-cadherin (Proteintech, 20874-1-AP), CD44 (Proteintech, 15675-1-AP), AKT (Cell Signaling Technology, 9272), phospho-Akt (Ser473, Cell Signaling Technology, 4060), CDK1/cdc2 (Cell Signaling Technology, 9116), phospho-CDK1/cdc2 (Tyr15) (Cell Signaling Technology, 4539), cyclin B1 (Cell Signaling Technology, 12231), P21 (Cell Signaling Technology, 2947), IGF2BP3 (Abcam, ab177477), ubiquitin (Cell Signaling Technology, 3936), DYKDDDDK Tag (Cell Signaling Technology, 14793), His-tag (Cell Signaling Technology, 12698), CUL2 (Proteintech, 10981-2-AP; Santa, sc-166506), and RPN2 (Abcam, ab244399).
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7

Western Blot Analysis of Protein Expression

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Antibodies to RNF114 (Millipore Sigma, HPA021184), p21 (Cell Signaling Technology, 12D1), GAPDH (Proteintech Group Inc., 60004–1-Ig), BRD4 (Abcam plc, Ab128874), DYKDDDDK Tag (Cell Signaling Technology, D6W5B) and beta-actin (Proteintech Group Inc., 6609–1-Ig) were obtained from various commercial sources and dilutions were prepared per recommended manufacturers’ procedures. Proteins were resolved by SDS/PAGE and transferred to nitrocellulose membranes using the iBlot system (Invitrogen). Blots were blocked with 5 % BSA in Tris-buffered saline containing Tween 20 (TBST) solution for 1 h at room temperature, washed in TBST, and probed with primary antibody diluted in recommended diluent per manufacturer overnight at 4 °C. Following washes with TBST, the blots were incubated in the dark with secondary antibodies purchased from Ly-Cor and used at 1:10,000 dilution in 5 % BSA in TBST at room temperature. Blots were visualized using an Odyssey Li-Cor scanner after additional washes. If additional primary antibody incubations were required the membrane was stripped using ReBlot Plus Strong Antibody Stripping Solution (EMD Millipore, 2504), washed and blocked again before being reincubated with primary antibody.
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8

Antibody Optimization for Western Blot, IHC, and IF

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The following antibodies were purchased from Cell Signaling and used at the indicated dilution for western blot analysis, immunohistochemistry, and immunofluorescence: pan-TEAD (13295, 1:1000), p38 MAPK (8690, 1:1000), phospho-p38 MAPK (4511, 1:1000), YAP (14074, 1:1000), TAZ (4883, 1:1000), Lats1 (3477, 1:1000), p-MK2 (3007, 1:1000), p-ERK (4370, 1:1000), DYKDDDDK tag (2368, 1:1000), Myc tag (2276, 1:1000), p38α (2371, 1:1000), p38β (2339, 1:1000), p38γ (2307, 1:1000), and p38δ (2308, 1:1000). The following antibodies were purchased from Santa Cruz Biotechnology and used at the indicated dilution for western blot analysis and immunofluorescence: YAP (sc-101199, 1:1000), HA (sc-7392, 1:5000), Myc (sc-40, 1:5000), GAPDH (sc-25778, 1:1000). TEAD4 (ab58310, 1:1000) was purchased from Abcam, Flag (A8592, 1:10,000) and vinculin (V9131, 1:5000) was purchased from Sigma, TEAD1 (610923, 1:1000) was purchased from BD Biosciences, Lats2 (A300-479A, 1:1000) was purchased from Bethyl Laboratories, and NFAT5 (bs-9473R OWL 1:1000) was purchased from One World Lab.
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9

Western Blot Analysis of FoxO1

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Cells were harvested in RIPA lysis buffer, and protein was quantified with the BCA assay (Beyotime). Whole-cell lysates containing 15 μg total protein were loaded onto 7.5% sodium dodecyl sulfate (SDS)-polyacrylamide gels, separated by electrophoresis, and transferred to polyvinylidene difluoride membranes (Millipore, Billerica, MA, USA). Nonspecific binding on the membranes was blocked with 5% bovine serum albumin (BSA) in TBS-T (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.1% Tween 20) for 1 h at room temperature. Membranes were then probed with primary antibodies (1 : 1000) against mouse FoxO1, DYKDDDDK Tag (Cell Signaling Technology, Danvers, MA, USA) and α-tubulin (Sigma) in blocking solution overnight at 4 °C. After washing with TBS-T, membranes were incubated with horseradish peroxidase-conjugated secondary antibodies (Santa Cruz Biotechnology, Santa Cruz, CA, USA) for 1 h at room temperature. Protein bands were visualized by exposing to an enhanced chemiluminescence detection system (LAS-4000 imager, Fujifilm, Tokyo, Japan) using the SuperSignal West Pico chemiluminescent substrate (Pierce, Rockford, IL, USA). Densitometry analyses were performed using ImageJ 1.42q software (National Institutes of Health), and the values for target proteins were normalized to α-tubulin as the endogenous control.
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10

Oxidative Stress Measurement Assays

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Malondialdehyde detection by lipid peroxidation MDA assay kit and ROS detection by reactive oxygen species assay Kit were provided by Beyotime Institute of Biotechnology (Nantong, Jiangsu, China). Polyvinylidene fluoride (PVDF) was from Millipore (Billerica, MA, USA). Dulbecco’s modified eagle medium (DMEM), fetal bovine serum (FBS), and phosphate-buffered saline (PBS) were products from Gibco (Australia). Lipofectamine™ 3000 was from Invitrogen (Thermo Fisher Scientific, Waltham, Massachusetts, USA). The primary antibodies for cleaved caspase-9, cleaved caspase-3, phospho-p44/42 MAPK (p-ERK1/2), AKT, Phospho-Akt (Thr308), Phospho-Akt (Ser473), DYKDDDDK Tag, snail and β-actin were purchased from Cell Signaling Technology (Danvers, MA, America). The primary antibodies for Cyt c and Cyt b5 were purchased from Abcom (Cambridge Biomedical Campus, Cambridge, UK). 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) was from Aladdin (Shanghai, China). The phosphatase inhibitor cocktail and protein inhibitor cocktail were from Beijing ComWin Biotech Co., Ltd. (Beijing, China). Confocal laser imaging was recorded on the Zeiss LSM 880, Western blot analysis was performed on the Tanon 5200, and OD value measurement was detected using SpectraMax Absorbance Reader.
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