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25 protocols using h4k20me1

1

Chromatin Profiling of Mouse Hippocampus

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Mouse hippocampus was harvested immediately after euthanasia. Chromatin immunoprecipitation was then performed as described in Broad ChIP protocol (http://www.roadmapepigenomics.org/protocols/type/experimental/). Briefly, tissues were minced and crosslinked in 1% formaldehyde (Thermo Scientific) for 15 min at room temperature and quenched with glycine for 5 min (Sigma). The samples were homogenized in cell lysis buffer containing proteinase inhibitors (complete, Roche) and chromatin was then fragmented to a size range of ~200–500 bp using a Branson 250 digital sonifier. Solubilized chromatin was then diluted and incubated with ~1 μg antibody at 4°C overnight. Immune complexes were captured with Protein A-sepharose beads, washed and eluted. Enriched chromatin was then subjected to crosslink reversal and proteinase K digestion at 65°C, phenol-chloroform extraction and ethanol precipitation. Isolated ChIP DNA was resuspended and quantified using the Qubit assay (Invitrogen). H3K4me1 (Abcam, ab8895), H3K4me3 (Millipore, #07-473), H3K9me3 (Abcam, ab8898), H3K27me3 (Millipore, #07-449), H3K27ac (Abcam, ab4729), H3K36me3 (Abcam, ab9050) and H4K20me1 (Abcam, ab9051) were used to immunoprecipitate endogenous proteins.
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2

ChIP-Seq and Western Blot Analysis

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Antibodies, H3K4me3 (clone MC315, Millipore 04-745), H3K27ac (Abcam Ab4729), H3K27me3 (clone C36B11, CST 9733), H4K8ac (Abcam Ab45166 for ChIP-Seq, IHC and western, Abclonal A7258 for western), H4K12ac (CST 13944), H3K27me1 (clone D3R8N, CST 84932), H3K23ac (CST 14932), H3K23me1 (Active motif, 39388), H3K9ac (clone C5B11, CST 9649), H3K9me2 (Abclonal A2359), H3K9me3 (Abcam ab176916), H3K4me1 (CST 5326), H4K20me1 (Abcam ab9051), H3K36me3 (Abcam ab9050), H4K20me3 (Abclonal A2372), H3 (Abcam Ab1791), p300 (Abcam ab14984), and β-actin (Abclonal AC026), were purchased from the indicated merchants.
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3

Comprehensive Antibody Validation for Research

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The following antibodies were used: TONSL (Abcam ab101898), TONSL (Sigma, HPA024679; validated in Extended Data Fig. 6d), MMS22L1 (link), H3 (Abcam ab1791, Abcam ab10799), GFP (Santa Cruz sc-8334, Abcam ab290), biotin (Abcam ab53494), MCM2 (BD Biosciences 610701), H2B (Abcam ab1790), H4K16ac (Millipore 07-329), H4K20me1 (Abcam ab9051), H4K20me2 (Cell Signalling 9759), 53BP1 (Santa Cruz sc-22760; Novus Biologicals NB100-904), γ-H2AX (Millipore 05-636), Cyclin B (BD Biosciences 610220), RPA70 (Abcam ab79398), SET8 (Millipore, 06-1304), MCM3 (Abcam ab 4460). Secondary antibodies conjugated with HRP were from Jackson ImmunoResearch Labs. Signals were revealed by chemiluminescence substrate from Pierce (SuperSignal West Pico or SuperSignal West Femto).
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4

Protein Expression Analysis in HUVEC Cells

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Proteins were extracted from the HUVECs of the different cultures by cell lysis buffer (Cell Signaling Technology, Danvers, MA). Equal amounts of protein were separated by 10% SDS–PAGE gels and then transferred to PVDF membranes (Millipore Corporation). The PVDF membranes were blocked in 5% skim milk at room temperature for 1 h and then incubated with the corresponding primary antibody (1:1000) at room temperature for 2 h. The primary antibodies were monoclonal antibodies against β-actin (ProteinTech, Wuhan, China), PTEN (ProteinTech, Wuhan, China), SET8 (ProteinTech, Wuhan, China), H4K20me1 (Abcam, Cambridge, UK), forkhead box protein O1 (FOXO1) (Cell Signaling Technology, Danvers, MA), and e-selectin (Santa Cruz Biotechnology, Santa Cruz, CA), and polyclonal antibodies against ICAM-1 (Cell Signaling Technology, Danvers, MA) and p-p65 (Cell Signaling Technology, Danvers, MA). The membranes were incubated with the corresponding secondary antibody (1:1000) at room temperature for 1 h. The membranes were then washed, and the proteins were detected by a LAS-4000 mini CCD camera (GE Healthcare).
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5

Antibody Validation for Western Blot and Immunofluorescence

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The following antibodies were used for western blot: BARD1 (Bethyl A300-263A, 1:500), BARD1 (Abcam ab64164, 1:500), SLF1 (Novus Biologicals NBP1-88358, 1:500), HA (HA.11, BioLegend 901513, previously Covance MMS-101P, 1:500), H4K20me2 (Diagenode C15200205, 1:3000), GFP (Roche 11 814 460 001, mixture of clones 7.1 and 13.1, 1:500), SET8 (Millipore, 06-1304, 1:1000), OsTIR1 (a gift from Masato Masato T. Kanemaki, 1:1000), Actin (Sigma A1978, 1:2000) and BRCA1 (Santa Cruz Biotechnology sc-6954, clone 9, 1:400). The following antibodies were used for immunofluorescence: BARD1 (Bethyl A300-263A, 1:500), BRCA1 (Santa Cruz Biotechnology sc-6954, clone 9, 1:400), 53BP1 (Santa Cruz Biotechnology H-300, 1:500), H4K20me1 (Abcam ab9051, 1:250; validated in Supplementary Fig. 2g), H4K20me2 (Diagenode C15200205, 1:250; validated in Supplementary Fig. 2g), H4K20me0 (Abcam ab227804, 1:10000; validated in Supplementary Fig. 2g), Phospho-H2A.X (S139) (Cell Signalling Technology 2577, 1:1000), HA (Roche 1 867 423, 1:200), HA (Bio Legend 901509, 1:100), BrdU (Eurobio ABC117-7513, 1:1000), and MCM2 (BD Biosciences 610701, 1:150).
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6

Immunostaining for DNA Damage Response

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Cells were grown on sterile 12 mm glass coverslips, fixed in 3% formaldehyde in PBS for 15 min at room temperature, washed once in PBS, permeabilized for 5 min at room temperature in PBS supplemented with 0.2% Triton X-100 (Sigma-Aldrich), and washed twice in PBS. All primary and secondary antibodies (Alexa fluorophores; Life Technologies) were diluted in filtered DMEM containing 10% FBS and 0.02% Sodium Azide. Antibody incubations were performed for 2 h at room temperature. After antibody incubations, coverslips were washed once with PBS and incubated for 10 min with PBS containing 4′,6-diamidino-2-phenylindole dihydrochloride (DAPI, 0.5 μg/ml) at room temperature to stain DNA. After three washing steps in PBS, coverslips were briefly washed with distilled water and mounted on 6 μl Mowiol-based mounting media. The following primary antibodies were used for immunostaining: H2AX Phospho S139 (mouse, 613401, 1:1,000; BioLegend), 53BP1 (mouse, Upstate MAB3802, 1:1,000), H4K20me2 (rabbit, ab9052, 1:100; Abcam), H4K20me1 (rabbit, ab9051, 1:200; Abcam), BRCA1 (mouse, sc-6954, 1:100; Santa Cruz), Cyclin A (mouse, sc-271682, 1:100; Santa Cruz), and RAD51 (rabbit, 70-002, 1:1,000; Bioacademia).
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7

Chromatin Profiling of Mouse Hippocampus

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Mouse hippocampus was harvested immediately after euthanasia. Chromatin immunoprecipitation was then performed as described in Broad ChIP protocol (http://www.roadmapepigenomics.org/protocols/type/experimental/). Briefly, tissues were minced and crosslinked in 1% formaldehyde (Thermo Scientific) for 15 min at room temperature and quenched with glycine for 5 min (Sigma). The samples were homogenized in cell lysis buffer containing proteinase inhibitors (complete, Roche) and chromatin was then fragmented to a size range of ~200–500 bp using a Branson 250 digital sonifier. Solubilized chromatin was then diluted and incubated with ~1 μg antibody at 4°C overnight. Immune complexes were captured with Protein A-sepharose beads, washed and eluted. Enriched chromatin was then subjected to crosslink reversal and proteinase K digestion at 65°C, phenol-chloroform extraction and ethanol precipitation. Isolated ChIP DNA was resuspended and quantified using the Qubit assay (Invitrogen). H3K4me1 (Abcam, ab8895), H3K4me3 (Millipore, #07-473), H3K9me3 (Abcam, ab8898), H3K27me3 (Millipore, #07-449), H3K27ac (Abcam, ab4729), H3K36me3 (Abcam, ab9050) and H4K20me1 (Abcam, ab9051) were used to immunoprecipitate endogenous proteins.
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8

ChIP Assay for Analyzing ELF3 and H4K20me1

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ChIP assays were implemented with a Simple ChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology, MA) according to the manufacturer’s instructions. In brief, HUVECs were fixed with 1% formaldehyde for 10 min at room temperature to mediate DNA and protein cross-linking. Glycine was then used to terminate the DNA and protein cross-linking reaction. Chromatin was sheared with the use of a Microson Ultrasonic Cell Disruptor XL (Misonix). Ten microliters of the sonicated solution was collected from each sample as input, and the remaining sample was incubated with anti-ELF3 (NOVUS, NBP1-30873), and anti-histone H4 lysine 20 methylation (H4K20me1; Abcam, ab9051) antibodies or a negative control IgG at 4 °C overnight. Immunoprecipitants were bound to protein G magnetic beads, and the DNA-protein cross link was reversed by incubating at 65°C for 2 h. Then, the DNA was purified, and enriched DNA sequences were analysed by qPCR. MARK4 oligonucleotide sequences for PCR primers were as follows: forward 5′-CCAACTGGGGAGAGAATGGG-3′ and reverse 5′-AGACTGAGAGAGACCCCAC-3′.
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9

Western Blot Analysis of Cellular Proteins

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Whole cells were washed with ice-cold phosphate-buffered saline, harvested, and resuspended in lysis buffer (Cell Signalling Technology, Danvers, MA). Protein samples were boiled for 10 min at 100 °C in sample loading buffer. Equal amounts of protein (50 μg) from different groups of HUVECs were separated by 8–10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to PVDF membranes (Millipore, Billerica, USA). Membranes were blocked with 5% skimmed milk solution for 1 h, and then all membranes were incubated with primary antibodies at 4 °C for 12 h. The primary antibodies used in the present study were as follows: monoclonal antibodies against β-actin (ProteinTech, Wuhan, China, 60004-1-Ig), KMT5A (ProteinTech, Wuhan, China, 14063-1-AP), CREB (Cell Signalling Technology, Danvers, MA, #9197), PTP1B (ProteinTech, Wuhan, China, 11334-1-AP), p-p65 (Signalway antibody, Maryland, #11014) and H4K20me1 (Abcam, Cambridge, UK, ab9051). After washing the membranes with PBST 5 times, an HRP-conjugated secondary antibody was added for 1 h at room temperature. Then, the membranes were washed five times with PBST, and the protein signal was detected by an ECL system.
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10

Antibody Validation for Western Blot and Immunofluorescence

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The following antibodies were used for western blot: BARD1 (Bethyl A300-263A, 1:500), BARD1 (Abcam ab64164, 1:500), SLF1 (Novus Biologicals NBP1-88358, 1:500), HA (HA.11, BioLegend 901513, previously Covance MMS-101P, 1:500), H4K20me2 (Diagenode C15200205, 1:3000), GFP (Roche 11 814 460 001, mixture of clones 7.1 and 13.1, 1:500), SET8 (Millipore, 06-1304, 1:1000), OsTIR1 (a gift from Masato Masato T. Kanemaki, 1:1000), Actin (Sigma A1978, 1:2000) and BRCA1 (Santa Cruz Biotechnology sc-6954, clone 9, 1:400). The following antibodies were used for immunofluorescence: BARD1 (Bethyl A300-263A, 1:500), BRCA1 (Santa Cruz Biotechnology sc-6954, clone 9, 1:400), 53BP1 (Santa Cruz Biotechnology H-300, 1:500), H4K20me1 (Abcam ab9051, 1:250; validated in Supplementary Fig. 2g), H4K20me2 (Diagenode C15200205, 1:250; validated in Supplementary Fig. 2g), H4K20me0 (Abcam ab227804, 1:10000; validated in Supplementary Fig. 2g), Phospho-H2A.X (S139) (Cell Signalling Technology 2577, 1:1000), HA (Roche 1 867 423, 1:200), HA (Bio Legend 901509, 1:100), BrdU (Eurobio ABC117-7513, 1:1000), and MCM2 (BD Biosciences 610701, 1:150).
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