The genomics team provides expertise to support the generation of genomics-based data. Our specialized labs and experienced staff offer a full suite of genomics services. We partner with the bioinformatics team to provide a streamlined set of complete services.
The Genomics & Bioinformatics Resource will be obsolescing our Illumina iScan BeadArray system on May 31st 2022. After May, we will no longer be supporting Infinium array processing, including genotyping and whole genome methylation arrays (EPIC). For alternative support options, please reach out to us.
The genomics team, in partnership with our bioinformatics colleagues, provides end-to-end support of Illumina next-generation sequencing projects. Our integrated resources are here for you every step of the way, from experimental design to library prep and downstream analysis.
The sequencers we have to support this work include an Illumina NovaSeq 6000, two NextSeq 2000s, and two MiSeqs. We offer a multitude of library preps including, but not limited to, bulk RNA-seq, single-cell RNA-seq (10x Genomics), RNA exome, polysome profiling, whole exome and whole genome sequencing, cell-free DNA, and targeted amplicon sequencing.
We also offer Cleavage Under Targets and Release Using Nuclease (CUT&RUN), an antibody-targeted chromatin profiling method developed by the Hutch’s Henikoff Lab to examine genome-wide occupancy of transcription factors and chromatin modifying proteins. CUT&RUN has been automated as AutoCUT&RUN, and we offer sample-to-Illumina library processing using a Beckman Biomek FX liquid-handling robot to facilitate high-throughput processing of 96 samples in two days.
Our experienced team will also work with you to develop and implement custom sequencing approaches.
The PacBio Sequel IIe is a third-generation sequencing platform that employs Single Molecule, Real-Time (SMRT) Sequencing technology to provide real-time single-molecule sequencing without the need for sample amplification. The Sequel IIe can deliver up to 4M-long reads with high consensus accuracy and is ideal for de novo genome sequencing, single-base modification detection, and pooled amplicon sequencing. We offer both SMRTbell library preparation and sequencing services.
The Genomics Resource also provides capillary electrophoresis-based sequencing and fragment analysis services. Two options, "full-service" and "ready-to-go" sequencing services are available.
With Ready To Go service, you set up and perform the sequencing PCR (Polymerase chain reaction) and we perform the cleanup, and analysis.
With Full Service, you provide a pre-mix of DNA template plus primer, and we perform the sequencing PCR, clean up, and analysis.
For fragment analysis, investigators run the reactions in their own lab and bring to Genomics for analysis on the 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), data is typically available the next business day.
We offer a full suite of single-cell sequencing assays, utilizing 10x Genomics technology, including Single-Cell RNA Seq, ATAC-Seq, Multiome ATAC + GEX, and Immune Profiling. 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), cDNAs, or 10x barcoded libraries.
We also offer 10x Genomics Chromium Controller training for labs wishing to independently run 10x experiments and have access to the controller 24/7.
In partnership with Experimental Histopathology, the Genomics Resource offers full-service end-to-end support of spatial transcriptomics, utilizing 10x Genomics Visium technology or Nanostring's GeoMx.
Visium support includes tissue qualification, tissue optimization, and the complete spatial gene expression workflow from tissue sectioning and placement through library prep and sequencing. We support both fresh-frozen and FFPE workflows. Before ordering your Visium kit, we highly recommend you reach out to us to set up a consultation and tissue qualification.
The GeoMx is a multi-cell profiler designed for high throughput, high plex studies. The GeoMx can profile >100 proteins and >18,000 RNAs with user-defined regions of interest. Additionally, the GeoMx is optimized for FFPE tissues. We offer end-to-end support for both the NGS and nCounter workflows.
The genomics team provides access to self-service qPCR (real-time PCR) instruments located in DE-341. Four ABI QuantStudio5 Real Time PCR Systems (two 96-well blocks and two 384-well blocks) 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 access the instructions below.
We offer digital gene-expression analysis using a staff-operated Nanostring nCounter automated system. The flexible system detects RNA, miRNA and DNA from a variety of sample types, including FFPE and whole-cell lysates. Both catalog and custom Codesets can be used.
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 have shRNA libraries for high-throughput genome wide screens, individual hairpins in GIPZ and other vectors to validate screen hits and investigate gene function, and provide training in the use of this material. An online searchable database and ordering system has been established to facilitate purchase of individual clones. Please note that access to the collection is limited to Fred Hutch labs only.