The ISCRM Genomics Core features the most advanced sequencing capabilities available today. Our sequencing instrumentation, including the latest equipment from 10X and Illumina, produces the highest quality, unbiased possible data about gene expression, regulation, and cell behavior. Whether you are interested in single-cell genomics or spatial genomics, our staff is here to provide the training and experimental design support you need to achieve your research objectives.
The ISCRM Genomics Core is available to all ISCRM faculty members and trainees. We are located on the fifth floor of the S Building on the South Lake Union campus.
The ISCRM Genomics Core provides a full sequencing pipeline, from tissue or single cells to analysis. The pipeline includes a 10x Chromium with Visium capabilities for library generation and cell encapsulation and an Agilent TapeStation 4200 for quality control, sequenced by an Illumina NextSeq 2000 capable of reads in the 400 million to 1.1 billion range. The final data output is analyzed by a full featured range of applications hosted on a ISCRM reserved node of the UW Hyak supercomputer.
The ISCRM Genomics Core provides all the equipment needed to perform all of the pipeline steps. The end-user only needs to provide consumables such as plastics, reagents, and the kits and cartridges from 10x, Agilent, and Illumina.
The instrumentation is complex, but Genomics Core staff will guide you through the process. The TapeStation also provides checks during several parts of the pipeline, catching user mistakes before expensive parts are used. The Visium system pairs nicely with the ISCRM Histology center, and allows for high quality sectioning.
Once the library generation is complete and cells are barcoded for the sequencer, use of the Illumina NextSeq 2000 is relatively straightforward – simply do the math for the number of cells per sample, how many samples, and the desired saturation (gene coverage). Once that is determined you pool your samples, place the pool into the cartridge, and the run starts. It takes 20-40 hours to generate 300GB-1TB of data, which is then transfered to the ISCRM Hyak node where the end-user can analyze the data according to the specifications desired, resulting in an unbiased, high quality data output.
*The ISCRM Genomics Core does not currently offer services for fee. Users must supply reagents and consumables and are responsible for conducting experiments with guidance from Mary as needed. Arrangement for analysis should be made as a part of experimental planning – Mary can help with or lead analysis, but due to limited bandwidth this is often not the fastest option.
Experimental planning, training
Independent analysis (minimal to moderate assistance)
Collaborative analysis (comprehensive assistance)
ISCRM Genomics Slack channel (user-driven knowledge base)
Fred Hutch Data Science Lab Slack channel (extensive knowledge base pertaining to data handling and analysis open to UW faculty, staff, and trainees)
ISCRM Genomics Core Compatible Kits and Consumables
Kits available from Illumina
Kits Available from Agilent
All Agilent 4200 TapeStation assays require loading tips, strip tubes with separate cap strips, as well as assay-matched ScreenTape, ladder, and sample buffer. Agilent reagents can be ordered through VWR.
Compatible Pipettes Tips
The core has Rainin Pipet-Lite LTS Pipettes, which require Rainin LTS-compatible tips (they are not compatible with universal tips). Additionally the tips listed are compatible with 10X Genomics GEM (Gel Bead-in-emulsion) handling – tips not validated by 10X Genomics may compromise emulsions and assay results (a complete list here).
10X Genomics Sales
Matt Rockwell, email@example.com, 425-395-5361
10X Genomics Science & Technology Advisor
Daphne Cooper, firstname.lastname@example.org, 916-717-8638
ACD Bio (RNAScope) Sales
Wade Patterson, Wade.Patterson@bio-techne.com, 206-245-6833
Kevin Harema, email@example.com, 720-201-1961
Partek Flow Account Manager
Kelly Kyle, firstname.lastname@example.org, 314-884-6157
Partek Flow Technical Support
ISCRM is excited to share yet another funding opportunity made possible through the generosity of the John H. Tietze Foundation.
The Genomics Core Pilot Awards is an award of up to $12,500 intended to support the research of any UW FACULTY member of ISCRM pursuing novel experiments in the areas of genomics, epigenomics, transcriptomics, or other next generation sequencing (NGS)-based methods.
Applications are now closed. Instructions on how to apply can be found here.