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For system help please email Penn’s iLab support at: iLab.Support@pennmedicine.upenn.edu

 

 

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Penn Genomics and Sequencing Core - Next-Generation Sequencing Laboratory

Status

We are functioning normally.  Data downloads are via HPC access or PennBox shared folders.

We have a new name to reflect the fact that we are now part of PGSC (formerly PGAC). The merger was done to better coordinate sequencing services at PSOM.

RRID (Research Resource Identifier)

Our RRID is RRID:SCR_022382 .  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

Where is my QC, Data, and Meta Data?

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.

News

2022-07-01 Kyia Rutherford has left the NGSC.

2022-07-01 The NGSC is now part of the Penn Genomics and Sequencing Core (PGSC).

2022-06-01 Kyra Kovacic is our newest NGSC staff member.

2022-06-15 The sequencing room door is now locked and requires card-reader permissions to access.

2021-10-18 Olga Smirnova, a 15-year veteran of the FGC and NGSC, has taken a new position at Penn. 
We thank Olga for her excellent unmatched service.  Best wishes!

2021-01-11 Our NextSeq has been retired and is no longer available for self- or full-service operations.

2021-01-11 Kyia Rutherford officially started at the NGSC.

2020-11-10 Our 10X Genomics Single Cell controller has been repaired and is available again
for self-service usage.  It is capable of running the new V3.1 reagents.

2020-11-06 We have had our first self-service runs on the NovaSeq!  Please contact us to
schedule your training - classroom and hands-on.  If you have already completed
the classroom training in the Spring or more recently, we can connect you with
Ana to set up the hands-on training.

2020-11-01 New lower prices for NovaSeq runs have been in place since September 1, 2020 and
are now posted in iLab and on our website.  A few other services have lower
prices as well, including 10X single-cell reagents.

2020-10-26 Joe Kutch, a 4-year veteran of the NGSC has recently take a new position at
Penn.  We thank Joe for his dedicated and excellent service to the NGSC.  Best
wishes!

 

COVID-19 Operating Level

We are open for Fall Resumption operations as of mid-September 2020 following the guidelines from UPenn/PSOM.

1. We are accepting new samples.
    * We have resumed our standard 11-12 (Tuesday to Friday) and 2:30-3:30PM (Monday to Thursday) drop-off windows.
    * You must submit a sample submission spreadsheet and receive confirmation before scheduling sample drop-off.
    * You must observe social distancing during the drop-off.
2. Self-service operations are available with limitations.
    * The rooms containing such equipment do not allow for more than single occupancy.
    * Equipment must be scheduled via our iLab calendars.
    * Sanitizing materials and procedures will be posted.
    * Equipment and work surfaces must be sanitized as per the instructions.
3. Hands-on training for the NovaSeq is available.

 

Overview of Services

We offer comprehensive high-throughput sequencing services from experiment design to basic data analysis.

This includes RNA extraction, library preparation, sample quality checks, and Illumina sequencing on our NovaSeq or MiSeq.

Both of these sequencers can be operated by clients in a self-service mode or by NGSC staff.

You can request training on the machines on the Request Services tab above.

We perform both bulk and single-cell experiments using our 10x Chromium controller.

We can generate very long read data with our Oxford Nanopore Technologies minION sequencer.

Informatics Services

The NGSC does not offer informatics services, but these other fine folks do:

PGAC/MPF - John Tobias - Part of our sister core facility PGAC.

IDOM 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.

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.

New customers are encouraged to schedule a consultation through this calendar.

 

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. Consultation Calendar
  3. Email us

 

Contacts

Name Role Phone Email Location
Jonathan Schug, Ph.D.
Technical Director
 
215 898 0773
 
jschug@pennmedicine.upenn.edu
 
12-156 Smilow
 
Tapan Ganguly, Ph.D.
Director
 
215-573-7238
 
gangulyt@pennmedicine.upenn.edu
 
B16 Anat-Chem Bldg.
 

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