Quantitative Analysis of DNA Modifications

LC-MS/MS analyses were performed as reported27 (link). Briefly, 1 μg of genomic DNA or S9.6 immunoprecipitated DNA was digested with a mixture of nuclease P1 (Roche), snake venom phosphodiesterase (Worthington) and alkaline phosphatase (Fermentas). One hundred nanograms of digested DNA were subjected to LC-MS/MS analysis. Data were normalized using internal isotopic standards for each 5mC oxidation derivative.

Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link: Access Free Full Text.

Arab K., Karaulanov E., Musheev M., Trnka P., Schäfer A., Grummt I, & Niehrs C. (2019). GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nature genetics, 51(2), 217-223.

Publication 2018

nuclease P1 snake venom phosphodiesterase alkaline phosphatase

Alkaline phosphatase Genomic Isotopic Ms ms Snake venom phosphodiesterase

Corresponding Organization : Institute of Molecular Biology

Other organizations : DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg University

Top 5 similar protocols

Variable analysis

independent variables

Amount of genomic DNA or S9.6 immunoprecipitated DNA (1 μg)

dependent variables

Levels of 5mC oxidation derivatives measured by LC-MS/MS analysis

control variables

Digestion of DNA with a mixture of nuclease P1, snake venom phosphodiesterase, and alkaline phosphatase
Use of internal isotopic standards for normalization of data

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!