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8 protocols using cdk4 sc 260

1

Western Blot Analysis of Signaling Proteins

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The total proteins were extracted with lysis buffer solution supplemented with protease inhibitors and phosphatase inhibitors (Pierce, USA) and quantified by the BCA protein assay (Pierce, USA). Each sample (30 μg) was separated by 10% SDS-PAGE, and then transferred to nitrocellulose (NC) membranes (PALL, USA). After blocking with 5% BSA in Tris-buffered saline-Tween 20, the membrane was incubated with primary antibody for overnight at 4°C. PHRF1 (ab85974) was purchased from Abcam. Akt (sc-8312), p-Akt (sc-33437), TGIF (sc-9084), p38 (sc-535), p-p38 (sc-17852-R), p21 (sc-397), cyclin A (sc-751), cyclin B1 (sc-752), cyclin D1 (sc-718) and CDK4 (sc-260) were purchased from Santa Cruz Technology. Rb (#9313S), p-Rb (#8516S), c-Myc (#13987S), p65 (#8242S) and PTEN (#9188S) were purchased from Cell Signaling Technology. After incubation with peroxidase-coupled anti-rabbit-IgG (ZSGB-BIO, Beijing, China) at room temperature for 1h, the protein bands were visualized by Bio-Rad Clarity™ western ECL substrate (Bio-Rad, USA) in the ChemiDoc™ XRS+ Imaging System (Bio-Rad, USA). Antibody to β-actin (1:1000, Santa Cruz Technology, sc-8432) was used as a loading control.
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2

Analyzing Protein Expression via Immunoblotting

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To analyze protein expression in cells, immunoblotting analysis was performed as previously described [2 (link)]. Antibodies against the following proteins were obtained from Santa Cruz Technology (California, US): Aur A (sc-25425), Aur B (sc-25426), BRCA1 (sc-6954), CDK2 (sc-163), CDK4 (sc-260), CDK6 (sc-177), cyclin D1 (sc-718), cyclin E (sc-247), cyclin A (SC-751). Antibodies against BRCA2 (19791-1-AP) and cyclin B1 (cs-4135) were obtained from Proteintech (Chicago, USA) and Cell Signaling Technology (Massachusetts, US), respectively. The detection of β-actin (A2228, Sigma Aldrich, St. Louis, MO) was used as a loading control. The secondary antibodies were F(ab)2 fragments of donkey anti-mouse immunoglobulin or of donkey anti-rabbit immunoglobulin linked to horseradish peroxidase from Cell Signaling Technology (Massachusetts, US). Immunoblotting reagents were from an electrochemiluminescence kit (Amersham Biosciences). To test whether the expression levels of proteins were regulated through proteasome-mediated degradation, cells were exposed with 20 μM MG132 (#S2619, Selleck Company, Texas, America) for 3 h and then harvested for Western blotting analysis.
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3

Comprehensive Immunohistochemical Analyses of Intestinal Tissues

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IHC and IF were performed as described previously (Dai et al., 2000 (link)), using formalin-fixed and paraffin-embedded jejunal sections and the following antibodies: human p16 (JC2, Jim Koh, Duke University), mouse p16 (M156, Santa Cruz Biotechnology, Santa Cruz, CA, USA) BrdU (IHC: Becton Dickinson, #347580; IF: Abgene), activated Caspase 3 (#9661, Cell Signaling Technology, Danvers, MA, USA), lysozyme (Dako, # EC.3.2.1.17), chromogranin A (Immunostar, #20085), PCNA (#2586, Cell Signaling), phospho-histone H3 (#9071, Cell Signaling), cyclin D1 (sc-753 (cross-reacts with cyclin D2, Santa Cruz), Cdk4 (#sc-260 (Santa Cruz), and γH2AX (#05-636, EMD Millipore, Billerica, MA, USA). Lgr5-lacZ expression was assayed by a modification of methods described previously (Barker et al., 2007 (link)). Freshly excised tissue was fixed in 2% neutral buffered formalin/0.2% glutaraldehyde/0.01% deoxycholate/0.2% NP40 for 30 min at RT, then incubated in X-gal substrate at RT overnight in the dark before embedding in paraffin. SAβgal staining was at pH 6.0. For p16 IB and Cdk4 IP, intestinal epithelial cells were isolated by treatment of excised tissue with EDTA (Weiser, 1973 (link)) and protein extraction with E1a lysis buffer (Harlow et al., 1985 (link)). For IB of γH2AX, mucosa was scraped off with a razor blade and chromatin extracts sheared by sonication.
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4

Western Blot Analysis of Protein Expression

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Cells were treated as described in the corresponding section of Results and then lysed by boiling for 10 min in sample buffer (2% SDS, 10% glycerol, 10% β-mercaptoethanol, bromphenol blue and Tris-HCl, pH 6.8). Lysates were fractionated on polyacrylamide gels and transferred to nitrocellulose. The blots were probed with specific antibodies followed by secondary antibody then membranes were examined using the LI-COR Odyssey infrared imaging system (LI-COR Biotechnology, Lincoln NE). The AR (N20, sc-816 and H280, sc-13062; 1:1,000), HSP90 (sc-7947; 1:1,000), and Cdk4 (sc-260; 1:1,000) antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). The HSP70 (1776-1; 1:5,000), HSP40 (3532-1; 1:1,000) and ubiquitin (1646-1; 1:1,000) antibodies were purchased from Epitomics (Burlingame, CA). p23 (ab92503; 1:1,000) and Hop (ab126724; 1:1,000) antibodies were purchased from Abcam (Cambridge, MA). Akt (4691; 1:1,000) and HDAC6 (7558; 1:1,000) antibodies were purchased from Cell Signaling Technology (Danvers, MA). CDC37 (4222S; 1:1,000) antibody was purchased Biogot Biotechnology Co., Ltd (Shanghai, China). The β-actin antibody (1:10,000) was purchased from Sigma (St Louis, MO). The secondary antibody was conjugated with IRDye 680/800 (Millennium Science; 926–32221, 926–32210; 1:10,000). Uncropped western blots are shown in Supplementary Fig. 13.
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5

Protein Quantification and Analysis

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Puromycin and G418 were purchased from Cayman Chemical Company (Ann Arbor, MI, USA). NEM and doxorubicin was purchased from Sigma-Aldrich Corporation (St. Louis, MO, USA). CHX and Mg132 were obtained from MedChemExpress (Shanghai, China). The following antibodies were used for either western blotting or immunohistochemical analysis: FBXO22 (13606–1-AP, Protein-tech, Wuhan, China), CDK2 (SC-748, Santa Cruz Biotechnology, CA, USA), CDK4 (SC-260, Santa Cruz Biotechnology, CA, USA), cyclinE1 (EP435E, Abcam, Cambridge, MA, USA), and GAPDH (KC-5G4; Kang Chen Bio-tech, Inc., Shanghai, China). The following antibodies were purchased from Cell Signaling Technology, Inc. (Beverly, MA, USA): Akt (C67E7), phospho-Akt (Ser473) (D9E), Erk (137F5), p38 (D13E1), phospho-p38 (3D7), p70s6k (49D7), phospho-p70s6k (1A5), cyclin B1 (V152), cyclin D1 (92G2) and p21(12D1).
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6

Comprehensive Protein Expression Analysis

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Protein expression levels were analyzed by standard Western blotting protocols. The following antibodies were used in this study: hBD3 antibody (500-P241) from PeproTech (Rocky Hill, NJ, USA); AKT (pan) (#4691), ERK 1/2 (#9102), phospho-AKT (#2965), phospho-ERK1/2 (#4376), p65 (#8242) and phospho-p65 (#3033) antibodies from Cell Signaling Technology (Danvers, MA, USA). Cyclin A (sc-596), cyclin E (sc-247), Cdk2 (sc-163) and Cdk4 (sc-260) from Santa Cruz Biotechnology (Dallas, TX, USA); β-actin (SP124) antibody from Sigma-Aldrich (USA). Cyclin D1/D2 was from R&D Systems (Minneapolis, MN, USA).
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7

Investigating Cell Cycle Regulation

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Antibodies against Cdk2 (sc-163), Cdk2 Thr 160 (sc-101656), Cdk6 (sc-53638), Cyclin E (sc-481), Cdk4 (sc-260), Rb (sc-102), Rb S780 (sc-12901-R) and Rb S807/811 (sc-16670-R): Santa Cruz Biotechnology. Anti Flag (A2220) and Actin (A2066): Sigma Aldrich. Cyclin D1 (DCS-11), Ki67 (PA1-21520): ThermoFisher Scientific. p27kip1(610241): BD Biosciences. Cleaved Caspase-3 (9661S): Cell Signaling Technology. β-Galactosidase (ab203749): Abcam. The p27 pY88 antibody and its specificity for p27 pY88 was previously described (16 (link)). K2i (sc-221409): Santa Cruz Biotechnology. Skp2i C1 (4817): R&D Systems. Palbociclib (PD 0332991) (HY-50767A), Letrozole (HY-14248): MedChem Express. Brki (531000): EMD Millipore. NMS (normal mouse serum) (Invitrogen, 31880) and NRS (normal rabbit serum) (Invitrogen, 31883) were used as isotype controls for monoclonal or polyclonal antibodies respectively.
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8

Comprehensive Molecular Profiling of Stem Cells

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Roswell Park Memorial Institute-1640 (RPMI-1640) medium, penicillin-streptomycin solution, and trypsin-EDTA (0.05%) were purchased from Gibco (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Tannic acid (TA; Cas. No: 1401-55-4), fetal bovine serum (FBS; 12003C), Zb (Z3902), and primary antibodies specific for SOX2 (MAB4423), OCT4 (MABD76), and NANOG (MABD24) were purchased from Sigma-Aldrich (Merck KGaA, St. Louis, MO, USA). Antibodies specific for β-actin (sc-47778), TRAIL (sc-8440), TRADD (sc-46653), Wnt5A (sc-365370), Casp8 (sc-81656), Bcl-2 (sc-7382), p21 (sc-756), cyclin E (sc-481), and CDK4 (sc-260) and secondary antibodies (anti-mouse (sc-516102) and anti-rabbit (sc-2357)) were obtained from Santa Cruz Biotechnology, Inc. (Dallas, TX, USA). The Wnt8A (H00007478-B01P) antibody was obtained from Abnova (Taipei City, Taiwan); pEGFR (#2234), β-Catenin (#9582), GSK-3β (#9315), Bax (#2772), Casp9 (#9502), C-Casp9 (#9505), Casp3 (#9662), C-Casp3 (#9661), cytochrome C (#11940), and p27 Kip1 (#3686) antibodies and a TCF/LEF Family Antibody Sampler Kit (#9383) were purchased from Cell Signaling Technology, Inc. (Beverly, MA, USA). Finally, DR4 (ab8415), DR5 (ab8416), and cyclin D1 (ab6152) antibodies were purchased from Abcam (Cambridge, MA, USA).
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