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15 protocols using ab4461

1

Western Blot Analysis of Tissue Samples

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For tissue samples, about 0.2 g of tissue was grinded into powder in liquid nitrogen. Protein extracts of frozen tissue powder and cells were prepared by using RIPA buffer in the presence of proteinase inhibitor cocktail (Sigma, St. Louis, MO, USA). Total protein extracts were separated by SDS-PAGE and transferred onto nitrocellulose membranes (Millipore, Bredford, USA). Anti-REG3A (Abcam, Ab134309), anti-MCM2 (Abcam, Ab4461), anti-MCM3 (Abcam, Ab128923), anti-PRAP1 (Abcam, Ab118186), anti-PRAP2 (Abcam, Ab176330), anti-pAKT(Cell Signaling Technology (CST), #4060, Danvers, MA, USA), anti-AKT (CST, #4691), anti-pERK1/2 (CST, #9101S), anti-ERK1/2 (CST, #9102S) and anti-GAPDH (CST, #5174) were used in Western analysis in accordance with the manufacturer's instruction. Signals were visualized with enhanced chemiluminescenct substrate (ECL, BioRad, Richmond, CA, USA) by exposure to films.
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2

Visualizing Retinal Cell Proliferation

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Click-iT EdU imaging kit (Invitrogen, C10337) was used according to the manufacturer's protocol in order to visualize cells undergoing S-phase during the time-window under study. 3-D RCs were incubated with 50 µg of EdU diluted in PBS for 1hr or 20 hr, then collected and processed for microscopic imaging. An antibody against the DNA replication licensing factor MCM2 (rabbit, 1:1000, Abcam, ab4461) was used to identify proliferating retinal progenitors, whereas an antibody against Phospho-Histone H3 (PH3, rabbit, 1: 250, Cell Signaling, #9701L) was used to identify cells in M phase by immunohistochemistry as described above.
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3

Immunohistochemical Analysis of Gonadal Tissue

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The gonads were fixed with 4% PFA and dried on filter paper, then soaked in Tissue-Tek O.C.T. compound (Sakura Finetek Europe B.V.) before snap frozen in isopentane (2-methylbutane) cooled with liquid nitrogen. Sections were made at 5–10 µm thickness by Leica 1950 Cryostat. The sections were fixed again in 4% PFA, then permeabilized in 0.2% Triton X, blocking in 5% donkey serum. Antigen retrieval was performed in 10 mm pH 6.0 Trisodium Citrate (Sinopharm) at 75°C for 30 min as previously described (63 (link)). The sections were incubated with the HTR1B antibody (Bioss, bs-1125R, 1:500), DRD4 antibody (Boster, A00998-2, 1:500), MCM2 antibody (Abcam, ab4461, 1:200), and βIII-tubulin antibody (R&D Systems, MAB1195-SP, 1:500) overnight at 4°C and the corresponding secondary antibodies conjugated to Alexa Fluor 555 (Invitrogen, 1:500) for 2 h at room temperature. DAPI (50 μm) was used for nuclear staining (64 ). Three random sections were collected and five representative images were taken from each gonad, and MCM2+ cells were counted.
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4

Automated Immunohistochemistry Staining Protocol

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Benchmark Ultra (Ventana Systems, Phoenix, AZ, USA) was used for the automatic staining procedure. Antigen retrieval and exposure were achieved by incubating the slides in TRIS solution at 95–100 °C for 36–64 min. Immunohistochemical staining was performed by incubation for 32 min with the following antibodies: NP-1 [Rabbit anti-Human Neuropilin-1 antibody Clone EPR3113 (ab81321, Abcam, Cambridge, UK) (diluted 1:80)]; MT [Mouse anti-Human Metallothionein antibody Clone E9 (M0639, DAKO, Glostrup, Denmark) (diluted 1:200)], E-Cadherin [Mouse anti-Human E-Cadherin antibody Clone 4A2C7 (180223, Invitrogen, Waltham, MA, USA) (diluted 1:80)], Ki-67 [Mouse anti-Human Ki67 antibody Clone 7B11 (180192z, Life Technologies, Carlsbad, CA, USA) (diluted 1:100)], and MCM2 [Rabbit anti-Human MCM2 polyclonal antibody (ab4461, Abcam) (diluted 1:600)]. The secondary reaction analysis was performed according to the manufacturers recommended protocol iVIEW DAB detection kit (760-091 Ventana Systems, Phoenix, AZ, USA) or OptiVIEW DAB detection kit (760-700 Ventana Systems, Phoenix, AZ, USA). Hematoxylin was used as a counterstain.
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5

Comprehensive Protein Extraction and Analysis

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Cells were lysed using (9 M urea, 50 mM Tris–HCL, pH 7.5, 150 mM β-mercaptoethanol) followed by sonication using a Soniprep 150 sonicator. Samples were resolved by SDS-PAGE and transferred to PVDF or nitrocellulose. Protein concentrations were determined by Bradford assays via spectrophotometry using a DeNovix DS-11 FX + spectrophotometer. Immunoblots were carried out using the indicated antibodies: α-Tubulin (Sigma, B-5-1-2; T5168, 1:100,000), BLM (Bethyl, A300-110A 1:2000), DNA2 (Abcam ab962488, 1:1000), EXD2 (Sigma, HPA005848, 1:1000), MCM2 (Abcam, ab4461, 1:10,000), MRE11 (Abcam, ab214, 1:1000), MUS81 (Abcam, ab14387 1:1000), POLD3 (Abnova, H00010714-M01, 1:500), RAD52 (28045-1-AP, Proteintech, 1:2000), SMARCAL1 (Santa Cruz, sc-376377 1:1000), SLX4 (University of Dundee, DU16029, 1:200), Vinculin (Thermo-Fisher, MA5-11690, 1:1000).
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6

Characterization of MCM Protein Expression

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For WB, the detailed procedures were performed as described previously [8] using the following primary antibodies: anti-MCM2 (Abcam, ab4461), anti-MCM3 (Abcam, ab128923), anti-MCM4 (Abcam, ab4459), anti-MCM5 (Abcam, ab75975), anti-MCM6 (Abcam, ab201683), anti-MCM7 (Abcam, ab2360), anti-CDK9 (Abcam, ab76320), anti-CyclinD1 (Abcam, ab16663), anti-CyclinE1 (Abcam, ab33911), anti-p53 (Abcam, ab241566), anti-p21 (Abcam, ab109502), anti-p27 (Abcam, ab32034), and anti-GAPDH (Abcam, ab181602).
For IHC, the standard method was described previously.14 (link) Slides were incubated with primary antibodies (Abs) against MCM2 (Immuway, YM6642), MCM3 (Abcam, ab128923), MCM4 (Immuway, YT2681), MCM5 (Abcam, ab75975), MCM6 (Abcam, ab190948), and MCM7 (Abcam, ab2360).
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7

Immunostaining Analysis of Brain Sections

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Immunostaining analyses were carried out on 16 μm brain coronal cryosection. The harvested samples were immersed in MOPS/EGTA/Magnesium Sulfate/Formaldehyde Buffer (MEMFA) overnight at 4°C, then rinsed with 1× PBS and cryopreserved in 30% sucrose in 1× PBS at 4°C. Samples were snap-frozen in Tissue-Tek (4583, Sakura, Torrance, CA, USA) and stored at −80°C. Cryosections were preserved at −20°C.
For BrdU staining, sections were treated with 2M HCl at 37°C for 10 min to denature the DNA. They were then washed five times with 1× PBS for 20 minutes each and blocked with 5% donkey serum in 1× PBS/0.3% Triton X-100. Afterward, immunofluorescence staining was performed following the standard protocol. The following primary antibodies were used against the corresponding antigens: SOX2 (1:500, ab97959, Abcam, Cambridge, UK), CDC42(1:200, sc-8401, Santa cruz, Santa cruz, CA, USA), NEUN (1:500, MAB377, Sigma, St. Louis, MO, USA), TUJ1 (1:500, MAB1195, R&D system, Minneapolis, MN, USA), ZO-1 (1:500, 33-9100, Invitrogen, Waltham, MA, USA), BrdU (1:500, MA3-071, Thermo Fisher Scientific, Waltham, MA, USA), MCM2 (1:300, ab4461, Abcam, Cambridge, UK), and TNC (1:100, MT1, DSHB, Iowa, IA, USA).
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8

Cell Lysis and Protein Immunoblotting Protocol

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Cell lysis was carried out in urea buffer (9 M urea, 50 mM Tris HCL, pH 7.3, 150 mM β-mercaptoethanol) followed by sonication using a soniprep 150 (MSE) probe sonicator. In some instances, cells were lysed in SDS loading buffer (2% SDS, 10% (v/v) glycerol, 2% 2-Mercaptoethanol and 62.5 mM Tris-HCl, pH 6.8) followed by boiling for 10 min. Samples were resolved by SDS-PAGE and transferred to PVDF or nitrocellulose. Protein concentrations were determined by Bradford assay by spectrophotometry using a NanoDrop 2000 device (Thermo Scientific). Immunoblots were carried out using the indicated antibodies: α-Tubulin (Sigma, B-5-1-2; T5168, 1:100,000), BRCA1 (Millipore, OP-92, 1:1000), BRCA2 (Millipore, OP-95, 1:1000), EXD2 (Sigma, HPA005848, 1:1000), MCM2 (Abcam, ab4461, 1:10,000), MRE11 (Abcam, ab214, 1:1000), PCNA (Santa-Cruz, PC-10, 1:500), RECQ1 (Santa Cruz, sc-166388,1:1000) and SMARCAL1 (Santa Cruz, sc-376377 1:1000).
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9

Antibody Validation for Stem Cell Research

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Antibodies used in this study were: anti-MERVL-gag (A-2801, Epigentek), anti-Pou5f1 (sc-5279; Santa Cruz Biotechnology), anti-Nanog (A300-397A, Bethyl), anti-Tubulin (12G10, DSHB), anti-Ezh2 (5246, Cell Signaling), anti-H3K4me3 (ab8580, Abcam), anti-H3K27me3 (9733, Cell Signaling), anti-Flag (F1804, Sigma-Aldrich), anti-Mcm2 (ab4461, Abcam), and anti-Flag (F1804, Sigma).
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10

Western Blot Analysis of Cell Signaling Proteins

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Proteins (20–50 µg) were loaded on a polyacrylamide gel and then transferred onto Immobilon-P. Membranes were incubated with homemade rabbit polyclonal antibodies raised against recombinant full length 6His-human Ensa protein (anti-hEnsa) (1/1000), phospho-Arpp19/Ensa S67/S71 (Cell Signaling, #5240, 1/250,), human Greatwall (anti-hGreatwall) (1/1000), phospho-Greatwall S87534 (link), α-Tubulin (1/1000 clone C102, generous gift of J.M. Andreu, Spain), Treslin (1/1000, Bethyl Laboratories Inc., A303-472A), phospho-Ser CDK substrate (1/1000, Cell Signalling, #9477S), Histone H3 (1/500, Santa Cruz, Biotechnology Inc., SC-FL136), Cdk1 (1/1000, Santa Cruz, Biotechnology Inc., SC-954), MCM-2 (1/10000, Abcam, ab4461), MCM-3 (1/2500, Abcam, ab4460), MCM-4 (1/5000, Abcam, ab4459) and MCM-5 (1/5000, Abcam, ab17967). Mouse monoclonal used are MCM-7 antibody (1/1000, Abcam, ab2360), Flag M2 (1/500, Sigma, F3165), Vinculin (1/1000, Sigma,V9131 Hvin-1) and β-Tubulin (1/500, clone E7, generous gift from N. Morin). Uncropped scans of all the western blot membranes are supplied in the Supplementary Information file.
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