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 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, three NextSeq 2000s, and three 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.
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 variety of DNA library preparation services for downstream sequencing on our Illumina and PacBio platforms. Our services include whole genome sequencing, whole exome sequencing, targeted panel sequencing, shotgun metagenomics, and 16S rRNA gene sequencing. We accept purified DNA from a variety of sample types including FFPE tissues and cell-free DNA.
We also offer Automated Cleavage Under Targets and Release Using Nuclease (AutoCUT&RUN) service, 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. We accept samples that have been treated with antibody and bound to ConA beads. We then use a Beckman Coulter Biomek i7 liquid-handling robot to facilitate high-throughput library preparation of up to 96 samples in two days.
Our experienced 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.
We provide bulk RNA-seq library preparation and sequencing services using poly-A capture for high-quality RNA and can accommodate samples with RNA input masses as low as 10 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 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 offer training and access to our 10x Genomics Chromium X and Chromium Controller for users who wish to independently perform scRNA-seq library preparation. Trained users have 24/7 access to the controllers.
We provide Multiplexed Array Sequencing/Kinnex library preparation services for PacBio sequencing, which concatenate smaller DNA fragments into longer libraries for HiFi sequencing. The full-length RNA kit uses total RNA as input. The single-cell RNA kit is compatible with cDNA generated using the 10x Genomics Chromium Next GEM Single Cell 3’ kit (v3.1) and Single Cell 5’ kit (v2) and is intended for use on a 3,000 to 10,000 cell library with 15-75 ng of cDNA as input. Both RNA-based kits enable sequencing of full-length RNA transcripts and are useful for evaluating alternative splicing and abundances of isoforms. Additionally, the 16S rRNA kit provides the ability to sequence entire 16S rRNA genes for microbiome studies.
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.
Genomics offers qualitative and semi-quantitative analysis of DNA and RNA using the Agilent 4200 Tapestation.
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.