At the genome center at Emory University, scientists credit the Pippin Prep with shaving almost a full day off the sample prep process for Illumina’s mate-pair library prep.
Chad Haase, laboratory manager at the Emory GRA Genome Center, says that the Sage Science Pippin Prep size selection instrument his lab acquired about a year ago has replaced the 16-hour runs that had previously been done on gels with a very low agarose concentration.
Jamie Davis, a scientist at the genome center, says that she typically runs the Pippin “after we do our first end repair and the biotinylation reaction.” Size selection generally takes about an hour, she says.
The Pippin Prep also works well for 454 sequencing. Haase’s team had tried another automated gel system, but it wouldn’t work for fragments larger than 1 kb. “Once we started making the large mate-pair libraries — 3 kb, 8 kb, and 20 kb fragments — then we had to come up with something different and the Pippin system was the best,” he says.
“With the large kb mate-pair libraries, the Pippin has really been our savior there,” Haase says. “A sample prep process that used to take us three days, we can now get down to roughly two days.”
Haase says that his team also uses the Pippin before amplicon sequencing on the Roche/454 GS-FLX Titanium. “If you have any small fragments whatsoever in a 454 amplicon library, it’s going to ruin the run,” he says. “The emulsion PCR prior to sequencing is preferential to smaller fragment amplification, so you’d get a whole bunch of 50-base-pair sequencing reads” without using the Pippin for size selection.