Genomics Services

PacBio Revio Sequencing (SCRI Collaboration)

Through our collaboration with Seattle Children’s Research Institute (SCRI), we offer access to the PacBio Revio sequencing platform, a seamless end-to-end service for investigators. Fred Hutch’s Genomics Shared Resource handles library preparation and coordinates direct delivery of prepared libraries to SCRI for sequencing.

This streamlined workflow ensures high-quality data generation while minimizing effort for the end user.

The Genomics Shared Resource provides capillary electrophoresis-based sequencing (Sanger Sequencing) and fragment analysis services. Users have access to one of two sequencing service options: the Ready to Go service option, and the Full Service option.

With the Ready to Go service, you set up and perform the sequencing PCR (Polymerase chain reaction) and we perform the cleanup and analysis of the PCR product.

With the Full Service option, you provide a pre-mix of DNA template plus primer and we perform the sequencing PCR, clean up and analysis.

For fragment analysis, you run the reactions in your own lab and bring your samples to the Genomics Shared Resource for analysis on our instrument.

Sequencing and fragment analysis are performed using two staff operated Applied Biosystems (ABI) 3730xl DNA Analyzers.

When dropped off by 4:00 pm (Mon-Fri), results are typically available the next business day.

We offer Automated Cleavage Under Targets and Release Using Nuclease (AutoCUT&RUN) and Automated Cleavage Under Targets and Tagmentation (AutoCUT&Tag) services. These antibody-targeted chromatin profiling methods were developed by Fred Hutch’s Henikoff Lab to examine genome-wide occupancy of transcription factors and chromatin-modifying proteins. We accept samples that have been treated with antibody and bound to ConA beads. We use a Beckman Coulter Biomek i7 automated liquid handling robot to facilitate high-throughput library preparation of up to 96 samples in two days.

Our team will also work with you to develop and implement custom sequencing approaches. Please contact us prior to submitting samples to discuss your project goals, our process and logistics.

Download more information about AutoCUT&RUN

We provide bulk RNA-seq library preparation and sequencing services using poly-A capture for high-quality RNA sequencing. We can accommodate samples with RNA input masses as low as 10 picograms (pg) of total RNA. Additionally, we provide RNA exome library preparation, which uses a hybridization capture approach to target coding genes and is compatible with low-quality RNA inputs isolated from FFPE tissues. We recommend contacting us prior to submitting samples to discuss the appropriate RNA sequencing method for your project.

We support the full suite of 10x Genomics single cell sequencing assays including 3’ and 5’ gene expression profiling, ATAC-Seq, Multiome ATAC + GEX, Immune Profiling and Single Cell Gene Expression Flex for fixed samples. We can assist with experimental design, cell prep best practices and sequencing coverage calculations.

We accept samples at various stages of the 10x workflow including cells, Gel Beads in Emulsion (GEMs), cDNA or 10x barcoded libraries.

We also provide end-to-end support for the 10x Genomics Flex Apex assay for fixed RNA. We accept samples that have been fixed and frozen in accordance with 10x Genomics guidelines and perform all downstream processing including probe hybridization, cell encapsulation, library preparation, and sequencing.

We also offer training and access to our 10x Genomics Chromium X Controller for users who wish to independently perform scRNA-seq library preparation. Trained users have 24/7 access to the controllers.

We provide library preparation and sequencing services using the Olink Reveal Proteomics assay. This technology using oligonucleotide-conjugated antibodies to detect >1000 proteins and is compatible with a variety of biological matrices including plasma and serum. Using an automated processing method developed in-house, we can run projects spanning one or more Olink Reveal plates. Our service includes library preparation, sequencing and data analysis.

The genomics team provides self-service access to multiple nucleic acid quantification technologies including:

• Two ABI QuantStudio5 Real Time PCR Systems (one each of 96-well and 384-well block configurations)
• A BioRad QX200 with AutoDG digital droplet PCR (ddPCR) system
• A Countable Labs single-molecule counting system

These systems are available 24 hours a day, with staff available for instrument training and to answer questions Monday through Friday, 9 a.m. to 5 p.m. To schedule time, please contact Genomics@fredhutch.org.

We provide material support, consultation and training in the use of gene modulation technology and precision, high-throughput liquid handling systems with applications ranging from high-throughput screens to investigating individual gene function and custom protocol development.

We provide shRNA libraries for high-throughput genome wide screens, as well as individual hairpins in GIPZ and other vectors to validate screen hits and investigate gene function. We also provide training in the use of this material.  An online searchable database and ordering system has been established to facilitate the purchase of individual clones.  Please note that access to the collection is limited to Fred Hutch labs only.