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6 protocols using ccnd3

1

Protein Expression and Quantification

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The cells were lysed using the mammalian protein extraction reagent RIPA (Beyotime, Beijing, China). Approximately a 50 μg protein extraction was separated by 10% SDS-PAGE, transferred to 0.22 mm nitrocellulose (NC) membrane (Sigma), and incubated with specific antibodies. Autoradiograms were quantified by densitometry using Quantity One software (Bio-Rad, CA, USA). β-actin (diluted 1:1000) antibody was used as a control and rabbit anti-FBXW7 (1:1000 dilution), p14 (1:100 dilution), p16 (1:100 dilution), p21 (1:150 dilution), p27 (1:50 dilution), CDK2 (1:200 dilution), CDK4 (1:100 dilution), CDK6 (1:100 dilution), c-myc (1:150 dilution), CCND1 (1:100 dilution), CCND2 (1:150 dilution), CCND3 (1:100 dilution), CCNE1 (1:150 dilution), CCNE2 (1:50 dilution) were provided by Cell Signaling Technology (MA, USA).
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2

Protein Expression and Apoptosis Assays

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Anti-phosphorylated and total FLT3, BTK (223), AKT, STAT5 and ERK, CCDN2, CCND3, CDK2, CDK4, CDK6, P53, γH2AX, P21WAF1/CIP1, CASPASE-3, CASPASE-7, CASPASE-8, PARP, Bad, Bax, Bcl-2, Bcl-XL, MCL-1, Pim-2, γ-H2AX, and β-actin antibodies were purchased from Cell Signalling Technology (Beverly, MA, USA). Pim-1 was obtained from Abcam (Cambridge, MA). Ibrutinib was obtained from Selleck Chemicals (Houston, USA). HHT was purchased from Sigma-Aldrich (St. Louis, MO, USA).
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3

Comprehensive Protein Quantification Protocol

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Blots were probed using the following primary antibodies: anti-eIF4E (Santa Cruz Biotechnology, Santa Cruz, CA, USA; sc-9976), anti-eIF4A1 (Abcam, Cambridge, UK; ab31217), anti-eIF4B (Epitomics, Burlingame, CA, USA; 2232-1), anti-PDCD4 (Abcam, ab80590), anti-actin (Abcam, ab6276), CCND3 (Cell Signaling, Beverly, MA, USA; 2936), PI3KCA (Cell Signaling, 4249), CDC25B (Cell Signaling, 9525), NPM1 (Cell Signaling, 3542), GNAS (Abcam, ab83735), RPL27A (Abcam, ab74731), hnRNPA1 (Abcam, ab4791) and RPS25 (GeneTex, Irvine, CA, USA; 101526). Suitable secondary antibodies were used for chemiluminescence detection. Samples were analyzed from at least two independent experiments.
Films were scanned on an ImageScanner III using LabScan software (GE Healthcare) and proteins were quantified using ImageQuant software (GE Healthcare), or for Licor analysis, IRDye 680LT-conjugated secondary antibody (LI-COR Biosciences, Lincoln, NE, USA) was used, followed by scanning on the Odyssey system (LI-COR Biosciences).
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4

Immunohistochemical Analysis of Retinal Layers

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Immunostaining of frozen sections was done as described previously.19 (link) Briefly, retinas were enucleated and fixed with 4% paraformaldehyde for 20 minutes or 1 hour at room temperature, treated with 15% sucrose overnight, treated with 30% sucrose for 6 hours, embedded in OCT compound (Leica), and sectioned (10 µm thickness) using the cryostat (Leica, CM3050S). Primary antibodies used are mouse monoclonal antibodies anti-Glutamine synthetase (Chemicon), photoreceptor-specific nuclear receptor (PNR; ppmx), HuC/D (Molecular Probes), Ccnd3 (Cell Signaling), rabbit polyclonal antibodies anti-Calbindin 28k (Chemicon), Pax6 (BioLegend), sheep polyclonal antibody anti-Chx10 (Exalpha Biologicals), and rat monoclonal antibody anti-Cd9 (Santa Cruz Biotechnology). Signals of primary antibodies were visualized using appropriate secondary antibodies conjugated with Alexa 488 or Alexa 594 (Molecular Probes). To measure the thickness of inner nuclear layer (INL) and outer nuclear layer (ONL), the central area, close to the optic nerve head, in more than three sections of each sample was analyzed. The thickness at three different parts was measured in each section, and the average was calculated. The average of all samples in each experimental group was calculated and unpaired two-tailed t test was used to evaluate statistical significance.
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5

Protein Expression Analysis of YAP1 and Cell Cycle Regulators

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Protein was extracted from GAC cell lines and paired primary tissues using RIPA lysis buffer with proteinase inhibitor. Protein concentration was measured by the method of Bradford (Bio-Rad, Hercules, CA) and 20 μg of protein mixed with 2 × SDS loading buffer was loaded per lane, separated by 12% SDS-polyacrylamide gel electrophoresis. Horseradish peroxidase (HRP) substrate solution was used for signal detection (Millipore, Billerica, MA). YAP1 protein was detected with a monoclonal anti-YAP1 antibody (1:10000 dilution, ab52771, Abcam, Cambridge, MA). Other primary antibodies were obtained from Cell Signaling Technology (Danvers, MA), CCND3 (1:2000, #2936), CCNE1 (1:1000, #4129), CDK6 (1:2000, #3136), p21 (1:1000, #2946), p27 (1:1000, #2552), p-Rb(Ser807/811) (1:1000, #9308), cleaved PARP(Asp214) (1:1000, #9541), BCL2(1:1000, #2870). The secondary antibodies were anti-Mouse IgG-HRP (1:30000 dilution, 00049039, Dako, Glostrup, Denmark) and anti-Rabbit IgG-HRP (1:10000, 00028856, Dako). The Western blot bands were quantified by ImageJ.
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6

Cellular Protein Analysis by Western Blotting

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Cells were harvested and lysed in E1A whole-cell lysate buffer supplemented with protease inhibitor mixture (Sigma-Aldrich) and PR619. Western blotting concentration in lysates was determined using the bicinchoninic acid (BCA) assay and analyzed by SDS/PAGE using antibodies against CCND1 (#2978; Cell Signaling), USP22 (#ab195289; Abcam), USP2 (#8036S; Cell Signaling), CDK4 (#sc-260; Santa Cruz), CDK6 (#3136S; Cell Signaling), FLAG (#F3165; Sigma-Aldrich), HA (#sc-805; Santa Cruz), Ubiquitin (#sc-7905; Santa Cruz), RB (#sc-50; Santa Cruz), pRB (#sc-271930; Santa Cruz), ATXN7L3 (#A302-800A; Bethyl), GCN5 (#sc-365321; Santa Cruz), CCND2 (#3741T; Cell Signaling), CCND3 (#2936S; Cell Signaling), phospho-CCND1 (#3300T; Cell Signaling), FBXO4 (#YZ1779; YenZym Antibodies), CUL1 (#sc-11384; Santa Cruz), SKP1 (#2156; Cell Signaling), RBX1 (#4397; Cell Signaling), ACTIN (#sc-47778; Santa Cruz), β-CATENIN (#8480; Cell Signaling), GAPDH (#ab9485; Abcam), ORC2 (#559266; Pharmingen), and TUBULIN (#T9026; Sigma-Aldrich).
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