High-Throughput Genomic Mate Pair Sequencing

The high throughput genomic mate pair libraries from HMCLs were prepared by the Mayo Clinic Genome Core Facilities using the Illumina Mate Pair protocols and their available kit (Nextera Mate Pair Sample Preparation kit, Illumina)^{10 (link),24 (link)}, Then, two samples were run on one lane of an Illumina HiSeq2000 with 50 bp reads. The sequences were aligned to hg19 using BWA, and a BAM file containing only the clustered discordant reads with clustered mates was created. Breakpoints in the IRF4 locus with discordant reads were identified in the BAM file by visual inspection.

Free full text: Click here

Zhu Y.X., Shi C.X., Bruins L.A., Wang X., Riggs D.L., Porter B., Ahmann J.M., de Campos C.B., Braggio E., Bergsagel P.L, & Stewart A.K. (2019). Identification of lenalidomide resistance pathways in myeloma and targeted resensitization using cereblon replacement, inhibition of STAT3 or targeting of IRF4. Blood Cancer Journal, 9(2), 19.

Publication 2019

Nextera Mate Pair Sample Preparation kit HiSeq2000

Genome Genomic libraries Irf4

Corresponding Organization : Mayo Clinic

Other organizations : Mayo Clinic in Arizona, Mayo Clinic in Florida

Top 5 similar protocols

Variable analysis

independent variables

Preparation of high throughput genomic mate pair libraries from HMCLs using the Illumina Mate Pair protocols and Nextera Mate Pair Sample Preparation kit

dependent variables

Identification of breakpoints in the IRF4 locus with discordant reads in the BAM file

control variables

Alignment of the sequences to hg19 using BWA
Creation of a BAM file containing only the clustered discordant reads with clustered mates

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!