The Lewis-Sigler Institute for Integrative Genomics houses the Genomics Core Facility which provides researchers with access to “Next Generation” high-throughput DNA sequencing technologies. The staff provide consultation on experimental design, library preparation, and data analysis. The Genomics Core Facility works closely with the Bioinformatics staff in the Lewis-Sigler Institute to provide researchers with computing power and consulting services to analyze sequencing data.
The facility currently houses an Illumina NovaSeq 6000 and MiSeq, and is staffed to provide full sequencing service for researchers NGS experiments. In addition to sequencing some of the other services provided include:
Library preparation for DNA samples: genomic DNA, ChIP-seq, amplicon, linked reads on long DNA using 10X Genomics Chromium system
Library preparation for RNA samples: strand-specific RNA-seq, microRNA and small RNA-seq, rRNA-depletion, SMART-seq for low input RNA, single cell RNA-seq using 10X Genomics Chromium system
DNA Size selection and clean up through BluePippin or Ampure XP Beads
DNA and RNA sample QC by Bioanalyzer or TapeStation
The Facility also has several pieces of ancillary instrumentation that researches have access to upon initial training. These instruments include:
- Qubit 2.0
- Nanodrop 1000
- Moxi Go II flow cytometer
- Agilent Bioanalyzer
- Agilent TapeStation 4200
- Covaris LE 220
- BluePippin DNA size selection system
- Biotek Synergy Mx plate reader
- Real Time PCR using ABI 7900 HT (96 well) or ViiA7 (96 or 384 well)
- Bio-Rad QX200 AutoDG Droplet Digital PCR system
- Agilent Microarray Scanner with Surescan High-Resolution Technology
- BiomekFX Liquid Handling Robot
- Kingfisher Flex for DNA or RNA extraction
- Beckman-Coulter Avanti-JE High Capacity Centrifuge
The entire lab is ozone free protecting the dye integrity of labeled samples.
Contingency of operations plan for the Genomics Core Facility
The primary contact for the Genomics Core Facility is Wei Wang, the director, email@example.com, 609-258-6998. If he is not available during the limited operations, please contact Jessica Wiggins, the lab manager, firstname.lastname@example.org, 609-258-9365.
The Genomics Core Facility will continue to provide services and access to shared instruments as long as our lab and staff are available and doing so is permitted by the University. Longer turnaround time is likely due to potential shortage of staffing. Sequencing of user provided libraries will be put on top priority to best support the ongoing genomics research. For NovaSeq sequencing, request for whole flowcells is recommended over individual lanes to reduce the waiting time for other matching libraries. Users are encouraged to submit iLab request for genomics services at the earliest convenience so that the core facility can plan the work and order the required reagents to prevent processing delay. This is especially important for sequencing with uncommon parameters such as long read length (like NovaSeq 300nt or Miseq 600nt) or large read number (like NovaSeq S1 or S2 flowcell), as well as for library preparation on large number of samples which takes more hands-on time.
All core facility staff have been cross-trained on almost all of the genomics services provided and shared instruments. All major instruments in the Genomics core facility have been supported by Uninterruptible Power Supply to mitigate brief outage of electricity. Phone numbers of the core facility staff are posted on the iLab web page to provide technical help on shared instruments. Shutdown procedures for main instruments are summarized in the appendix of the contingency plan, and the procedure printout is attach to each instrument for everybody to follow in case the core facility staff are unavailable for an extended period.
In accordance with the university guideline on social distancing, in person training on shared instruments has been paused in general. Urgent need for training may still be accommodated upon request. The users can instead request the corresponding services provided by the core staff. Users are encouraged to use the sample drop off freezer set up in the core lab, instead of submitting samples to core staff in person. The core staff will try to maintain the recommended six feet distance when feasible, and may stagger their work time to some extent as 2 shifts (normal and late shifts which overlap) when needed.
In case our building or the entire campus were closed, the core facility staff who is able to work will continue to work remotely to support the genomics research. Users can log in to our iLab system at https://princeton.corefacilities.org/service_center/3970 to send internal messaging, or email email@example.com in which all core facility staff can communicate with users and to each other. In addition, the users can directly email the core facility director at firstname.lastname@example.org to obtain consultation on experimental design, data analysis, as well as collaboration on evaluating and developing new sequencing methods. All members of the core facility have exchanged cellular numbers for emergency communication. Instruments in the facility will be shut down when the entire campus is closed.
The core facility has requested the following online systems to be maintained functional at all times: HTSEQ database for sequencing data storage and delivery, local GALAXY system for data analysis, and iLab system for ordering and sample tracking.
To minimize the potential interruption of services due to significant disruption of supplies, the Genomics Core Facility has been ordering and stocking up consumables and reagents with no or long expiration as much as possible. For expensive reagents with limited shelf life, such as the Illumina sequencing kits, the facility will carefully monitor the usage and place frequent small orders to maintain the stock.