Penn Genomics and Sequencing Core - DNA Sequencing Laboratory

DNA Sequencing Facility is now part of Penn Genomics and Sequencing Core (PGSC).

Two other former cores, Next-Generation Sequencing Core (NGSC) and Molecular Profiling Facility (MPF) are also part of PGSC.

PGSC offers both Next-Generation and Sanger Sequencing services. Other services include Fragment Analysis, including human cell line authentication and, molecular profiling of DNA and RNA on ABI real-time PCR instrument and digital PCR on Qiagen Qiacuity.

Next-Generation Sequencing:

We offer comprehensive high-throughput next-generation sequencing services from consulting on experimental design to data analysis.

This includes DNA/RNA extraction, library preparation, sample quality checks, and Illumina sequencing on our NovaSeq 6000, NextSeq 2000 and MiSeq.

NovaSeq can be operated by clients in a self-service mode or by the core staff. For using both stages (self-service mode) please contact us.

NextSeq 2000 and MiSeq are run only by the core staff.

You can request training on NovaSeq 6000 on the Request Services tab above.

We perform both bulk RNA-Seq, and single-cell RNA-Seq experiments using our 10x Chromium Controller.

We can generate very long reads using our Oxford Nanopore Technologies minION sequencer. We also have access to a PromethION.

We are in the process of introducing long-read PacBio Revio services at the core. Please stay tuned.

For further information please contact Tapan Ganguly, Director and Erik Toorens, Technical Director.

 Sanger Sequencing:

Sanger samples should be delivered to our drop boxes in BRB lobby, Johnson Pavilion lobby, and Smilow lobby in a small plastic bag with printout of submission. Samples will be picked up at 11AM every weekday. Samples can also be delivered directly to our lab by 5PM M-F (excluding university holidays) at 502 Stellar-Chance Labs. 

Please use the link below to access our Sanger Submission site:

UPENN SANGER SUBMISSION SITE

Fragment Analysis and Genotyping, Human Cell Line Authentication: Jennifer Rosado

jmrosado@pennmedicine.upenn.edu

Mouse Genotyping and Molecular Biology work: Erik Toorens

toorens@pennmedicine.upenn.edu

NGS, BioAnalyzer, Pippin, Qubit: Erik Toorens and Jennifer Rosado

toorens@pennmedicine.upenn.edu

jmrosado@pennmedicine.upenn.edu

Real-Time PCR: Adam Bdeir

Adam.Bdeir@pennmedicine.upenn.edu

All other inquiries or questions about our services please contact:

Tapan Ganguly PhD (Facility Director) gangulyt@pennmedicine.upenn.edu

Erik Toorens (Technical Director) toorens@pennmedicine.upenn.edu

Overview of Services

DNA Sequencing Facility was founded in 1994 as an Abramson Cancer Center (ACC) core. In 2014, the Perelman School of Medicine (PSOM) and Abramson Cancer Center (ACC) combined two NCI CCSG supported cores, the DNA Sequencing Facility and the Molecular Profiling Facility to consolidate genomic services under a single umbrella Core. The resulting Shared Resource, the Penn Genomic Analysis Core was and continues to be directed by Dr. Tapan Ganguly.

DNA Sequencing Facility offers sequencing services on three platforms, gold standard Sanger sequencing on ABI capillary sequencers, next-generation sequencing (NGS) on Ion Torrent PGM and S5 and, Illumina MiSeq and Next-Seq. along with experimental design and data analysis.

The NGS service includes library preparation for multiple applications including targeted sequencing, RNA-Seq and Exome-Seq. Free consultation is provided for project planning and experimental design. Data analysis service is performed in consultation with the investigators.

The capillary sequencers also enable microsatellite genotyping and fragment analysis for VNTR, SNaPshot and Human Cell Line Authentication.

Guide to Ordering Services

Details of how to use iLab to order services are available in this Guide for Penn investigators. External users should use the guide for CHOP, Wistar, Monell, off-campus, for-profits. 

Research Resource Identifier (RRID)

Our RRID is RRID:SCR_024999. Please cite us using this identifier when publishing your results.

Leadership and Staff

Location and hours of operation

Links and Resources

1. https://genetics.med.upenn.edu/cores/genomic-analysis-core/
2. https://www.med.upenn.edu/cores/
3. https://www.pennmedicine.org/cancer/cancer-research/for-researchers/shared-resources

Contacts