Next-Generation Sequencing Core

NGSC Website and PMACS HPC Maintenance

Between Aug 17 and Aug 21 the PMACS High-performance Compute Cluster (HPC) was closed for a planned maintenance.  All downloads and data access should be functioning normally at this point.

COVID-19 Operating Level

We are open for Phase II operations as of July 13, 2020 following the guidelines from UPenn/PSOM.

1. We are accepting new samples from UPenn/CHOP clients.
    * We have canceled our standard 11-12 and 3-4PM drop-off windows.
    * Sample drop-off is by appointment only.
    * 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. We are accepting new samples from outside clients but have to prioritize Penn/CHOP samples over others.
3. Self-service operations, other than Illumina sequencers 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.
4. Illumina sequencers are available for self-service sequencing on a case-by-case basis.
5. Hands-on training for the NovaSeq is not yet availalbe.

 

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, NextSeq, or MiSeq.

All three 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.

Existing NGSC Clients

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.

New NGSC Clients

Start by reviewing our FAQ and how we work.

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

The PI and investigator will need accounts.

Additional information can be reviewed at the full core website.

Sample Drop-off Hours and Location

Drop-off Hours                                          Location                                                                                        
Tuesday - Friday 11 AM -12 PM     

Monday - Thursday 3 AM - 4 PM 
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.

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
 
Klaus Kaestner, Ph.D.
Director
 

 
kaestner@pennmedicine.upenn.edu
 

 

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