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.

Overview of Services

The Penn Genomics and Sequencing Core (PGSC) provides a spectrum of sequencing, genomics and molecular biological services with a team of highly experienced and trained professionals under a Director and Technical Director. The services include consultation on experimental design to performing experiment to downstream data analyses.

We offer Next-Generation Sequencing on multiple platforms:

Short Read - Illumina NovaSeq X Plus, NextSeq 2000 and MiSeq

Long Read - PacBio Revio and Oxford Nanopore MinION

This includes DNA/RNA extraction from different sources, library preparation with quality control, and sequencing followed by bioinformatics.

Applications include mRNA-Seq, total RNA-Seq, small RNA-Seq, WGS, targeted sequencing, ChIP-Seq on X Plus; WGS and whole methylome on PacBio etc.

For single-cell genomics we use 10X Genomics Controller; the applications include scRNA-Seq and snRNA-Seq. Soon we are going to introduce multiplexed scRNA-Seq. Multiome including scATAC-Seq are under development.

Bioinformatics support is available for both core and externally generated datasets.

Legacy Sequencing: Sanger Sequencing on ABI 3730xl capillary sequencer.

The capillary sequencer enables fragment analysis for microsatellite-based genotyping, human cell line authentication and other applications.

Targeted molecular profiling including genotyping and gene expression is performed using ThermoFisher QS6 Pro and Qiagen digital PCR instruments. Mouse genotyping is done using PCR-based approach.

For further information please contact Director, Tapan Ganguly, gangulyt@pennmedicine.upenn.edu and Technical Director, Erik Toorens, toorens@pennmedicine.upenn.edu.

Charges for Major NGS Services

Informatics Services 

The NGSC offers informatics services:

Please contact John Tobias – He will provide the service regardless of where the data is generated.

These other fine folks also provide service:

DOM DRC Functional Genomics Core - Jonathan Schug and Kirill Batmanov - Members of the Institute for Diabetes and Metabolism's (IDOM) Diabetes Research Center (DRC) can get a wide range of bioinformatics services via the Functional Genomics Core (FGC).

IBI - Bioinformatics Core - Taehyong Kim - The Bioinformatics Core in the Institute for Biomedical Informatics offers a wide range of services.  See the BiC website for more information.

 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