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8 protocols using anti cyclin a

1

Protein Quantification and Analysis Protocol

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Protein preparation and Western blots were performed as described previously15 . Nuclear and cytoplasmic lysates were prepared with the NE-PER kit (Pierce Biotechnology) according to the manufacturer’s instructions. The protein levels of active β-catenin in whole-cell lysates were quantified using the anti-active β-catenin clone 8E7 antibody (Millipore). The antibody is specific for the active form of β-catenin, dephosphorylated on Ser37 or Thr41. The following primary antibodies were used: anti-menin (1:1,000; Cell Signalling Technology), anti-β-catenin (1:1,000; Cell Signalling Technology), anti-active β-catenin (1:1,000; Millipore), anti-Phospho-β-catenin (Ser33/37/Thr41; 1:1,000; Cell Signalling Technology), anti-Phospho-β-catenin (Ser45; 1:1,000; Cell Signalling Technology), anti-α-tubulin (1:1,000; Cell Signalling Technology), anti-α-tubulin (1:1,000; Cell Signalling Technology), anti-Cyclin D2 (1:1,000; Cell Signalling Technology), anti-Cyclin A (1:1,000; Abcam), anti-Cyclin B2 (1:1,000; Santa Cruz Biotechnology), anti-Mcm2 (1:1,000; Cell Signalling Technology), anti-Pbk (1:1,000; Cell Signalling Technology), anti-C-myc (1:1,000; Cell Signalling Technology), anti-GAPDH (1:10,000; KANGCHEN) and anti-lamin B (1:1,000; Santa Cruz Biotechnology). Images have been cropped for presentation. Full size images are presented in Supplementary Figs 9–11.
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2

Immunoblotting for Cell Cycle Proteins

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Anti-preS1 (Aprogen, Daejeon, Korea), anti-cyclin A, anti-cyclin D1, anti-cdk2, anti-cdk4, anti-PCNA (Abcam, Cambridge, UK), anti-p53 and anti-β-actin (Santa Cruz Biotechnology Santa Cruz, CA, USA) antibodies were used for immunoblotting.
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3

Hepatocyte Protein Expression Analysis

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Hepatocytes were isolated by two‐step collagenase digestion and gradient centrifugation. Total protein of hepatocytes was extracted using RIPA lysis buffer (Beyotime, People's Republic of China). A total of 15 μg of protein/well were electrophoresed by 10% sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS‐PAGE). After the protein transfer was completed, the PDVF membranes were blocked with 5% non‐fat powdered milk at room temperature for 1 hours. Next, the PDVF membranes were incubated with anti‐Brg1 (1:10 000; Abcam), anti‐CDK1 (1:10 000; Abcam), anti‐CDK4 (1:2000; Abcam), anti‐cyclin A, (1:2000; Abcam), anti‐cyclin D1, (1:10 000; Abcam), anti‐cyclin E1, (1:1000; Abcam), anti‐LATS1, (1:5000; Abcam), anti‐p‐YAP, (1:5000; Abcam), anti‐YAP, (1:5000; Abcam) and anti‐GAPDH antibody (1:1000, Abcam) at 4°C overnight. GAPDH was used as an internal reference. Finally, enhanced chemiluminescence (ECL) (Thermo Fisher) was used to detect the expression of the target proteins.
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4

Western Blot Analysis of Cell Cycle Regulators

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For Western blot analysis, anti-CREB (1:1,000; Upstate, Darmstadt, Germany), anti-cyclin A (1:400; Abcam, Cambridge, MA, USA), anti-cyclin E (1:400; Santa Cruz Biotechnology, Dallas, TX, USA), anti-cyclin D1 (1:400; Santa Cruz Biotechnology), anti-cyclin-dependent kinase 2 (CDK2) (1:400; Santa Cruz Biotechnology), anti-CDK4 (1:400; Santa Cruz Biotechnology), and anti-CDK6 (1:400; Santa Cruz Biotechnology) antibodies were used.
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5

Whole-cell Lysate Preparation and Protein Analysis

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Whole-cell lysates were prepared using RIPA buffer as described previously [39 (link)] and analyzed using the following primary antibodies: anti-β-actin, anti-Sp1 (PEP2), anti-cyclin E, anti-ZEB1, and anti-GAPDH (Santa Cruz Biotechnology, Santa Cruz, CA, USA); anti-myc (Upstate Biotechnology, Lake Placid, NY, USA); anti-integrin α5 and anti-Tie2 (BD Biosciences, San Jose, CA, USA); anti-vimentin (Sigma, St Louis, MO, USA); anti-phospho-c-Jun N-terminal kinase (JNK) (T183/Y185), anti-phospho-extracellular signal-regulated kinase 1/2 (ERK1/2), anti-ERK1/2, anti-phospho-Akt (S473), anti-Akt, anti-survivin, anti-cyclin D1, anti-JNK, anti-phospho-VEGFR2 (Y996), anti-phospho-VEGFR2 (Y1175), anti-VEGFR2, anti-bcl-2, and anti-PARP (Cell Signaling, Danvers, MA, USA); anti-ZEB2 (6E5; Active Motif, Tokyo, Japan); anti-cyclin A, anti-bcl-2, anti-VEGF, and anti-phospho-c-Jun (Abcam, Cambridge, MA, USA); anti-ZO-3 (Invitrogen); and anti-E-cadherin and anti-phospho-Tie2 (R&D Systems, Minneapolis, MN, USA). Subcellular fractions were prepared using the Compartmental Protein Extraction Kit (Millipore, Billerica, MA, USA) according to the manufacturer’s instructions.
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6

Immunoblotting with Diverse DNA Damage Proteins

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The following primary antibodies were used: anti-FANCD2 (Abcam, ab2187), anti-FANCA (Bethyl, A301-980A), anti-Vinculin (Sigma, V9131), anti-ATR (Santa Cruz, sc-1887), anti-FANCI (Santa Cruz, sc-271316), anti-Actin (Santa Cruz, sc-1616), anti-BRCA1 (Santa Cruz, sc-6954), anti-CHK1 (Santa Cruz, sc-8408), anti-pCHK1 S345 (Cell Signalling, 23415), anti-FLAG M2 (Sigma, F1804), anti-γH2AX (Upstate, JBW3001), anti-CyclinA (Abcam, ab16726), anti-MYC tag 9E10 (Upstate, 05–419), anti-TRF1 (Abcam, ab10579), anti-RAD51 (CosmoBio, BAM-70-001-EX), anti-FANCJ (Sigma, B1312), anti-BRCA2 (Calbiochem, OP95), anti-ABRAXAS (Bethyl, A302-180A), anti-RAP80 (Bethyl, A300-763A). Anti-FANCG [67 (link)], FANCC [68 (link)], FANCE [69 (link)], FANCF [70 (link)] and FANCD2 pT691 [71 (link)] were gifts from Dr. Alan D’Andrea (Dana-Farber Cancer Institute, Boston). Anti-USP1 (C-ter) [38 (link)] was a gift from Dr. Tony Huang. Anti-PALB2 [72 (link)] was a gift from Drs. David Livingston and Bing Xia. Anti-FANCL and anti-FANCM were gifts from Dr. Weidong Wang.
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7

Antibody Source for Cell Signaling

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Anti-β-catenin and anti-p27kip1 antibodies were purchased from BD Biosciences (San Jose, CA, USA). Anti-Sox4, anti-Sox6, anti-Sox7, anti-Sox9, anti-Sox11, and β-actin antibodies were obtained from Sigma-Aldrich Chemicals (St. Louis, MO, USA). Anti-Snail and anti-Slug antibodies were from Cell Signaling (Danvers, MA, USA). Anti-p21waf1, anti-cyclin D1, and anti-CD44s antibodies were purchased from Dako (Copenhagen, Denmark). Anti-Sox2 and anti-cyclin A antibodies were from Abcam (Cambridge, MA, USA) and Novocastra (Newcastle, UK), respectively. Anti-HA and anti-E-cadherin antibodies were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA) and Takara (Shiga, Japan) respectively. Anti-CD133 antibody was from Miltenyi Biotechnology (Bergisch Gladbach, Germany).
STK2, which is a serum-free culture medium for mesenchymal stem cells, [22 (link)] was obtained from DS Pharma Biomedical (Osaka, Japan).
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8

Immunofluorescence Quantification of Cell Cycle Markers

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A549 or H4 cells were fixed in 4% paraformaldehyde immediately after treatment and then blocked with 10% normal donkey serum (Sigma-Aldrich) for 1 h, followed by overnight incubation at 4°C in primary antibodies: mouse anti-Ki-67 (Dako, United Kingdom); anticyclin A; anticyclin D; anticyclin E; antiBcl-2; antiBcl-xL; antiBad; antimammalian target of rapamycin (Abcam, United Kingdom); rabbit anticleaved caspase 3, 8, or 9; anti-α 2 -adrenoceptor; or antibenzodiazepine receptor (Abcam). Cells were washed with phosphate-buffered saline and then incubated in fluorescein isothiocyanate or rhodamine-conjugated secondary antibody (Merck Millipore, United Kingdom). Cells were counterstained and mounted with nuclear dye 4′, 6-diamidino-2-phenylindole-mounting medium (Vector Laboratories, USA). Images were captured under an Olympus BX4 microscope (United Kingdom). Fluorescent intensity was quantified with the mean pixel intensity of relevant antibody staining by ImageJ software (National Institutes of Health, USA). Ten representative regions per section were randomly selected by an assessor blinded to the treatment groups. Intensity values were calculated and expressed as relative to control.
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