Illumina Workflow: Pippin for ChIP-seq

As we continue our blog series on applications that are frequently used with Pippin size selection and Illumina sequencing, we move on to ChIP-seq. One of the most popular capabilities enabled by next-gen sequencing, ChIP-seq (or chromatin immunoprecipitation sequencing) is used to map protein binding sites or analyze protein-DNA interactions across entire genomes.

One of the earliest app notes for Pippin Prep came from Thomas Westerling at the Dana-Farber Cancer Institute. To learn more about the ChIP-seq library prep, check out the app note.

Pippin has also been used with large-scale ChIP projects, such as generating a complete picture of regulatory networks in Mycobacterium tuberculosis. This effort, tackled by James Galagan and his lab at Boston University, entailed methodically performing ChIP-seq on each transcription factor in the microbe to determine which other transcription factors and genomic regions were expressed as a result.

Chris Mawhinney, the scientist in Galagan’s lab who performed the work, told us that enlisting Pippin for these experiments saved time and eliminated the possibility of sample cross-contamination. “If you have too broad a range of sizes, the sequencer software has issues locating the clusters,” she said. “With Pippin Prep, you can get it down to a really nice, narrow size.” Proper sizing also removes adapter-dimers, which otherwise eat into sequencing capacity.

Mawhinney also told us that Pippin speeds up the sample prep routine. “The great thing about Pippin is that you can go right from size selection to PCR; there’s no middle cleanup step, so it’s very convenient,” she said.

We’ll continue our blog series in the coming weeks with posts on ddRADseq, Moleculo, and more. Check back soon!

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