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Sonicated calf thymus dna

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Sonicated calf thymus DNA is a laboratory reagent used in various molecular biology applications. It is extracted from the thymus gland of calves and mechanically sheared to reduce the length of the DNA fragments. This product provides a source of double-stranded DNA for use as a control or in experiments involving DNA-based techniques.

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Lab products found in correlation

Human histone octamer, by EpiCypher (2 mentions) H3k4me3, by EpiCypher (2 mentions) H3k4me1, by EpiCypher (2 mentions) H3k4me2, by EpiCypher (2 mentions) Image lab 4, by Bio-Rad (2 mentions) Ap substrate, by Merck Group (1 mentions) Millex ha filter, by Merck Group (1 mentions) Costar 96 well half area plates, by Corning (1 mentions) Ssdna, by Merck Group (1 mentions) Victor microplate reader, by PerkinElmer (1 mentions)

3 protocols using sonicated calf thymus dna

1

Chromatin Remodeling Assay with Labeled Nucleosomes

Cited 1 time
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The 216-bp DNA fragment containing 146-bp Widom601 sequence in the middle was P32 labeled by PCR amplification from the pGEM-3Z-601 vector12 (link). Four types of human histone octamer (wt, H3K4me1, H3K4me2, and H3K4me3) were ordered from EpiCypher, Inc.13 (link). Mono-nucleosomes were assembled onto the labeled template by salt serial dilution method as previously described14 (link). Cold mono-nucleosome (2 µM) was assembled using Xenopus laevis histones with unlabeled DNA fragment by the same method, which is then mixed with sonicated calf thymus DNA (1mg/ml, Sigma). 1 µl purified BAF complex (0.15 mg/ml) was incubated with 2 µl P32 labeled mono-nucleosomes (25 nM) at room temperature in final 10 µl remodeling buffer (20 mM Tris-HCl pH7.5, 50 mM NaCl, 2.5 mM MgCl2, 2 mM DTT, 100 µg/ml BSA, 5% Glycerol, 0.01% NP-40, 0.01% Triton X-100, and 1 mM ATP). After 30min, 1.5 µl cold nucleosome was added to quench the reaction for 30 minutes at room temperature. The reaction products were loaded onto 5% native polyacrylamide gels and resolved by electrophoresis at 4°C for 2.5 hours at 200 volts. Gels were exposed to storage phosphor screens and scanned with a Typhoon imaging scanner. Quantified calculations were done using the software of Image Lab 4.1 (Bio-rad). Error bars, mean ±SD n=4 replicates.
Local A., Huang H., Albuquerque C.P., Singh N., Lee A.Y., Wang W., Wang C., Hsia J.E., Shiau A.K., Ge K., Corbett K., Wang D., Zhou H, & Ren B. (2017). Identification of H3K4me1-Associated Proteins at Mammalian Enhancers. Nature genetics, 50(1), 73-82.
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2

Chromatin Remodeling Assay with Labeled Nucleosomes

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The 216-bp DNA fragment containing 146-bp Widom601 sequence in the middle was P32 labeled by PCR amplification from the pGEM-3Z-601 vector12 (link). Four types of human histone octamer (wt, H3K4me1, H3K4me2, and H3K4me3) were ordered from EpiCypher, Inc.13 (link). Mono-nucleosomes were assembled onto the labeled template by salt serial dilution method as previously described14 (link). Cold mono-nucleosome (2 µM) was assembled using Xenopus laevis histones with unlabeled DNA fragment by the same method, which is then mixed with sonicated calf thymus DNA (1mg/ml, Sigma). 1 µl purified BAF complex (0.15 mg/ml) was incubated with 2 µl P32 labeled mono-nucleosomes (25 nM) at room temperature in final 10 µl remodeling buffer (20 mM Tris-HCl pH7.5, 50 mM NaCl, 2.5 mM MgCl2, 2 mM DTT, 100 µg/ml BSA, 5% Glycerol, 0.01% NP-40, 0.01% Triton X-100, and 1 mM ATP). After 30min, 1.5 µl cold nucleosome was added to quench the reaction for 30 minutes at room temperature. The reaction products were loaded onto 5% native polyacrylamide gels and resolved by electrophoresis at 4°C for 2.5 hours at 200 volts. Gels were exposed to storage phosphor screens and scanned with a Typhoon imaging scanner. Quantified calculations were done using the software of Image Lab 4.1 (Bio-rad). Error bars, mean ±SD n=4 replicates.
Local A., Huang H., Albuquerque C.P., Singh N., Lee A.Y., Wang W., Wang C., Hsia J.E., Shiau A.K., Ge K., Corbett K., Wang D., Zhou H, & Ren B. (2017). Identification of H3K4me1-Associated Proteins at Mammalian Enhancers. Nature genetics, 50(1), 73-82.
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3

Quantification of Anti-dsDNA and Anti-ssDNA Antibodies

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Anti-dsDNA antibody levels in sera of patients and healthy controls were determined as previously described (54 (link)). Briefly, Costar 96-well half-area plates (Corning Inc., New York, NY) were dry coated overnight at 37°C with 25 µg/ml of sonicated calf thymus DNA (Sigma-Aldrich, St. Louis, MO) that had been filtered using a 0.45-µm Millex HA filter (Millipore, Germany) to remove ssDNA. Plates were blocked and then incubated with serum samples (1:50 and 1:100 dilutions, 25 µl/well). IgG+ or IgM+ anti-dsDNA antibodies were detected using alkaline phosphatase (AP)-labeled anti-human IgG or anti-human IgM antibody (Southern Biotechnology, Birmingham, AL) and developed with 50 µl/well AP substrate (Sigma-Aldrich). The optical density at 405 nm (OD405) was measured by using a Victor microplate reader (PerkinElmer, Waltham, MA). The enzyme-linked immunosorbent assay (ELISA) to determine the levels of anti-ssDNA antibodies was performed exactly as described above, except that the plates were coated with 25 µg/ml ssDNA (Sigma-Aldrich).
Hirako I.C., Gallego-Marin C., Ataide M.A., Andrade W.A., Gravina H., Rocha B.C., de Oliveira R.B., Pereira D.B., Vinetz J., Diamond B., Ram S., Golenbock D.T, & Gazzinelli R.T. (2015). DNA-Containing Immunocomplexes Promote Inflammasome Assembly and Release of Pyrogenic Cytokines by CD14+ CD16+ CD64high CD32low Inflammatory Monocytes from Malaria Patients. mBio, 6(6), e01605-15.
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