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Penn Genomics and Sequencing Core - Next-Generation Sequencing Laboratory

 

 

 

The prior Next Generation Sequencing Core (NGSC) is now part of Penn Genomics And Sequencing Core (PGSC).

Two other former cores, DNA Sequencing Facility (DSF) and Molecular Profiling Facility (MPF) are also part of PGSC.

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

NovaSeq Pricing png

 LibPrep

 pacbio pricing

 

 

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.

 

RRID (Research Resource Identifier)

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

Need Help?

Try these new links for help before, during, and after working with the NGSC.

PSOM iLab help - links to help for BAs and PIs

FAQs - answers to common questions.

URLs - links into the websites of Illumina, 10X Genomics, and others

 

We use iLab for equipment schedulingstarting an experiment, and for billing.

The science, quality checks, data delivery, FAQs, etc. is at our NGSC Website.  

Accounts for iLab and the NGSC data website are distinct and must be set up separately for PI and investigator.

Letters of Support

Contact us for letters of support for grant applications.

 

NGSC Websites

We are using iLab for equipment schedulingstarting an experiment, and for billing.

The science, quality checks, data delivery, etc. remains at our NGSC Website.

You will still need to use your NGSC accounts.

Take a look at our FAQ to see how we work.

 

Sample Drop-off Hours and Location

Drop-off Hours                                          Location                                                                                        
11:00AM-12:00PM - Tuesday to Thursday
2:30PM - 3:30PM - Monday to Friday

12-160 Smilow

3400 Civic Center Blvd., Philadelphia, PA 19104

POs

Make your remittance payable to Trustees of the University of Pennsylvania, Attn: Jeffrey Griffin.Other details pending.

 

Map of SCTR 12-th Floor

Map of SCTR 12th Floor

Links and Resources

  1. Core Website
  2. Email us

 

Contacts

Name Role Phone Email Location
Tapan Ganguly, Ph.D.
Director
 
215-573-7238
 
gangulyt@pennmedicine.upenn.edu
 
B16 Anat-Chem Bldg.
 
Erik Toorens
Technical Director
 
251-573-4832
 
toorens@pennmedicine.upenn.edu
 
502 Stellar-Chance Labs
 

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