DRIP Assay for R-loop Detection

DRIP was performed as previously described with modifications [28 (link)]. Briefly, the cells were collected and incubated with lysis buffer containing proteinase K. The fragmented DNA was incubated in immunoprecipitation (IP) buffer containing S9.6 antibody (Millipore) to capture the R-loop in vivo. Protein A-agarose beads (Millipore) were used to enrich DNA-RNA hybrids. Purified DNA was used to generate a library using the KAPA HiFi HotStart ReadyMix (Roche). qPCR was used to check the enrichment of S9.6 antibody at certain genomic locus. Sequences of all DRIP-PCR primers are listed in Supplementary Data 6.

Free full text: Click here

Jia Q., Tan Y., Li Y., Wu Y., Wang J, & Tang F. (2023). JUN-induced super-enhancer RNA forms R-loop to promote nasopharyngeal carcinoma metastasis. Cell Death & Disease, 14(7), 459.

Publication 2023

S9.6 antibody Protein A-agarose beads KAPA HiFi HotStart ReadyMix

Agarose Antibody Buffer Cells Genomic Hybrids Immunoprecipitation Library Primers Protein a Proteinase k R loop

Corresponding Organization :

Other organizations : Hunan Cancer Hospital, Central South University

Top 5 similar protocols

Variable analysis

independent variables

Lysis buffer containing proteinase K
S9.6 antibody (Millipore) in immunoprecipitation (IP) buffer
Protein A-agarose beads (Millipore)

dependent variables

R-loop enrichment
Expression of certain genomic loci

control variables

Not explicitly mentioned

controls

Positive control: Not specified
Negative control: Not specified

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!