NGSC FAQ Document
Jonathan Schug
NGSC Staff
| NGSC - FAQs |
Next-Generation Sequence Core Perelman School of Medicine | University of Pennsylvania |
|
NovaSeq 6000
Links
- NovaSeq Specifications (@Illumina)
- NovaSeq Scheduling Page (@iLab)
- NovaSeq Training Request (@iLab)
Introduction
Thanks to the support of about a dozen institutes, departments, and the PSOM, the NGSC has purchased an Illumina NovaSeq 6000.
The machine has been delivered and will be operational by the end of January.
The NovaSeq will be operated in both the standard full-service mode as well as in self-service mode following training.
The HiSeq 4000 that we currently operate will be decomissioned 2020-01-31.
If you have samples that have to be sequenced on the HiSeq 4000 please contact us ASAP.
Training
We plan to provide training by the following mechanisms:
- An initial large group introduction to the NovaSeq by Illumina staff.
- Smaller 4-person hands-on training sessions run by Illumina staff.
- Office hours run by Illumina staff.
- As-needed hands-on support by Illumina staff.
Of course the NGSC staff will always be available to answer questions.
Hands-On
General Information
The initial training schedule will include 3 hands-on training sessions with 3 to 4 people using SP flow cells. We are scheduling now.
Session One - January 27/28
Times, rooms, and contents as follows:
- Monday AM - 9am - 12pm SCTR 12-100
- Powerpoint presentations (Illumina sequencing information and NovaSeq workflow, patterned flow cell discussion)
- start NovaSeq wash
- Monday PM
- hands on: load NovaSeq
- Tuesday AM 9-11am, SCTR 12-120
- Troubleshooting, best practices, run reviews
- examples of good and bad NovaSeq runs
- Tuesday PM 2-5pm, SCTR 12-100
- Further discussion, other topics of interest.
We have the opporunity to sequence user samples. The flow cells can accomodate up to 250PE. If you are selected for this session please send along sample count and barcodes as soon as possible.
Scheduling
The NovaSeq will be scheduled via an iLab calendar at the NGSC iLab website.
You will be able to schedule time once you have been trained.
You can request training here.
Announcements
A list serve, ngsc-announcements@lists.upenn.edu, has been set up. Subscribe to the list to receive updates as we progress.
Contributors
| Person | Entity |
|---|---|
| Robert Vonderheide | Abramson Cancer Center |
| Dan Kelly | Cardiovascular Institute |
| Carl June | Center for Cellular Immunotherapies |
| Shelley Berger | Epigenetics Institute |
| Mitch Lazar | IDOM |
| John Wherry | Institute for Immunology |
| Andy Minn | Mark Foundation for Cancer Research |
| Rick Bushman | Microbiology |
| Ronny Drapkin | Ovarian Cancer Research Center |
| David Roth | Pathology and Laboratory Medicine |
| Dave Meaney | School of Engineering |
| Dan Rader | Department of Genetics |
| Jon Epstein | Perelman School of Medicine |
Time Line Photos
Some snapshots of the NovaSeq.
2019-12-20 - What’s in the box?.
2020-01-02 - NovaSeq as delivered.