Next-Generation Sequencing Core
(Perelman School of Medicine, University of Pennsylvania)
Klaus Kaestner, Ph.D. Director
Jonathan Schug, Ph.D. Technical Director
The Next-Generation Sequencing Core (NGSC) was founded to serve the high-throughput
sequencing needs of the University of Pennsylvania's Perelman School of Medicine (PSOM).
The services of the facility include consultation on experimental design, sample
preparation and quality control, analysis and interpretation of results for and nextgeneration sequencing experiments. The NGSC’s staff has been performing Illumina
sequencing since 2008. We have completed nearly 700 runs on our Illumina sequencers
for experiments using ChIP-Seq, small RNA-Seq, RNA-Seq, HITS-CLIP, bisulfite-sequencing,
genome resequencing using capture technology, and many others. The facility occupies
over 700 sq ft. in Dr. Kaestner's lab. We provide data and analysis results using our
password-protect website running on a large Linux server. We use the PSOM’s new 1000node cluster for data processing. Raw run data is backed-up on tape and at Amazon.
We have two Agilent bioAnalyzer 2100, an Agilent TapeStation, LifeTechnologies Qubit
fluorometer, and use the KapaBiosystems kit for sample and library quality assessments, 80˚C freezers for sample and reagent storage, 4˚C refrigerator for reagent storage, barcode
scanners and databases for reagent and sample tracking. We have a Biomek FP robot for
sample handling. We recently acquired a Fluidigm C1 system which is able to capture single
cells from which we can prepare single-cell RNA-Seq libraries.
The NGSC operates two (with overflow access to two more) hiSeq2000s which currently
offer up to 200 million single-end or 400 million paired-end reads per lane. We also have
two hiSeq2500s and a pair of miSeqs. We have tested and shared multiplexed ChIP-seq
library protocols to enable ChIP-seq experiments to take advantage of the capacity
hiSeq2000 to facilitate quantitative comparison of binding. We have also worked to
evaluate RNA-seq library preparation techniques for small amounts of RNA. We are
currently incorporating robotics to automate library preparation and quality control.
For data analysis, the NGSC offers a range of pipelines that use a mixture of academic and
custom tools to analyze data from ChIP-Seq, small RNA-Seq, mRNA-Seq, HITS-CLIP,
bisulfite-sequencing, and genome resequencing libraries and experiments. We have
additional high-level pipelines that perform differential comparisons using a detailed
experimental design that we capture for each experiment.
The NGSC, with the backing of the Perelman School of Medicine, is committed to staying on
the forefront of sequencing technology and computing support. Thus the capacity and
services of the NGSC will expand to meet demand from researchers at Penn.
2014/02/06