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.

Pipeline – From Cells to Data Output

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.

Using the Equipment – What to Expect

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.

Preparation

Experimental planning, training

  • Assistance with experimental design
  • Instrument training (Illumina NextSeq2000, Agilent TapeStation, 10x Chromium X)
  • Assistance with protocol/kit selection and preparations

Experimentation

Supported assays/methods

  • All 10x single cell assays (scRNAseq, scATACseq, scMultiome, etc)
  • 10x Visium assays
  • Most bulk RNAseq, ATACseq, ChIPseq and similar assay kits (check with Mary before ordering)
  • Library QC and quantification via qPCR, Agilent TapeStation, Qubit fluorometer
  • Sequencing of Illumina compatible libraries (on Illumina NextSeq2000)
  • Analysis findings validation via RNAscope ISH assays
  • Lab space and equipment for sequencing library preparation
  • Guidance for experiment execution and troubleshooting
  • New assays can be added when resources/capabilities allow

Analysis

Initial steps

  • Sequencing metrics evaluation
  • BCL to fastq conversion
  • Data transfer

Independent analysis (minimal to moderate assistance)

  • Hyak supercomputer node with RStudio and packages for sequence alignment, annotation, data QC, etc. (some command line coding required)
  • Template scripts and SOPs for Hyak node use
  • Partek Flow web-based software for bulk and single cell NGS analysis
  • Guidance/advising for analysis and troubleshooting

Collaborative analysis (comprehensive assistance)

  • Single cell, spatial, and bulk assay analysis in R or Partek Flow (first come, first serve basis with limited bandwidth)

Knowledge Community
ISCRM Genomics Slack channel (user-driven knowledge base)
https://iscrm-sequencing.slack.com/

Fred Hutch Data Science Lab Slack channel (extensive knowledge base pertaining to data handling and analysis open to UW faculty, staff, and trainees)
https://fhdata.slack.com/

ISCRM Genomics Core Compatible Kits and Consumables 

To ensure kit completeness and compatibility with your experiment please contact Matt Rockwell, matthew.rockwell@10xgenomics.com, and cc Mary, mregier@uw.edu

Kits available from Illumina 

To ensure you receive ISCRM discounts (25-40% off) on NextSeq2000 sequencing kits please request a quote from Kevin Harema, khamera@illumina.com, and cc Mary, mregier@uw.edu

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).

Vendor Support

10X Genomics Sales
Matt Rockwell, matthew.rockwell@10xgenomics.com, 425-395-5361

10X Genomics Technical Support
Daniel Hunter, daniel.hunter@10xgenomics.com, 206-607-9391
OR 10x Genomics Support Site https://www.10xgenomics.com/support
OR support@10xgenomics.com

10X Genomics Science & Technology Advisor
Daphne Cooper, daphne.cooper@10xgenomics.com, 916-717-8638

 ACD Bio (RNAScope) Sales
Wade Patterson, Wade.Patterson@bio-techne.com, 206-245-6833

Illumina Sales
Kevin Harema, khamera@illumina.com, 720-201-1961

Illumina Technical Support
Dakota Ahrendsen, dahrendsen@illumina.com, 253-318-2931
OR techsupport@illumina.com, 1-800-809-4566

Partek Flow Account Manager
Kelly Kyle, kkyle@partek.com, 314-884-6157

Partek Flow Technical Support
support@partek.com

Genomics Core Pilot Awards

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.

Contact For Equipment Usage & Training

Mary Regier, Director
mregier@uw.edu

To sign up for equipment, click here.