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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:
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.
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.
Our RRID is RRID:SCR_024999. Please cite us using this identifier when publishing your results.
Name | Role | Phone | Location | ||
Tapan Ganguly, Ph.D | Director | 215-573-7238 | gangulyt@pennmedicine.upenn.edu |
B16 Anat-Chem Bldg.
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Erik Toorens | Technical Director | 215-573-4832 | toorens@pennmedicine.upenn.edu | 502-503 Stellar-Chance Bldg. | |
Adam Bdeir | Research Specialist | 215-573-7407 | Adam.Bdeir@pennmedicine.upenn.edu |
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Jennifer Rosado | Research Specialist | 215-746-3333 | jmrosado@pennmedicine.upenn.edu | 502-503 Stellar-Chance Bldg. | |
Deborah Evans | Financial Coordinator | 215-573-7407 | dlmckinn@pennmedicine.upenn.edu | 502-503 Stellar-Chance Bldg. |
Hours | Location |
Monday - Friday 9 AM - 5 PM |
502-503 Stellar-Chance Bldg 422 Curie Blvd. Philadelphia, PA 19104 |
Name | Role | Phone | Location | |
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Tapan Ganguly |
Director
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215-573-7238
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gangulyt@pennmedicine.upenn.edu
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B16 Anat-Chem Bldg.
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Erik Toorens |
Technical Director
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215-573-4832
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toorens@pennmedicine.upenn.edu
|
Stellar Chance 502
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Price List |
► Genotyping & Fragment Analysis on Capillary Sequencer (1) | |||
Name | Description | Price | |
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Human Cell Line Authentication (1-2 cell lines, each line) |
Authentication is done using the Promega GenePrint® 10 kit. Several databases of human STR profiles are utilized for data analysis.
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Inquire |