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Shared Resources News

llumina NextSeq 2000 sequencing platform
llumina NextSeq 2000 sequencing platform Image courtesy Illumina

Genomics & Bioinformatics update

February 2021

The Genomics & Bioinformatics shared resource recently reduced pricing for several NovaSeq 6000 flow cells, resulting from streamlined reagent manufacturing and reduction of Illumina kit costs. Some run costs have reduced by as much as 27%.

Our recently added NextSeq 2000 now enables high-output mode which generates up to 1.1 billion read pairs with 50, 100, 200 and 300 cycle sequencing kits available. In addition to the increased output, custom sequencing primers can now be incorporated into both P2 and P3 output modes. Improved instrument efficiency and reagent packaging provide a ~25% cost reduction when compared to HiSeq 2500 Rapid runs. 

The genomics team continues to offer services for the full suite of 10x Genomics single-cell assays, including the new Single Cell Multiome ATAC + Gene Expression option which can measure gene expression and open chromatin simultaneously from the same cell, across thousands of cells.

The bioinformatics team is available for data analysis and consulting to help Cancer Consortium users make optimal use of this high-throughput instrumentation. Our group consists of three dedicated bioinformaticians with a wide range of expertise in standard applications such as RNA-seq, whole exome sequencing, ChIP-seq, CUT&RUN, CRISPR screens, and various single-cell analyses. We also provide consultation and bioinformatics support for more novel and customized workflows.

For questions or more information, please contact the genomics team at genomics@fredhutch.org and the bioinformatics team at bioinformatics@fredhutch.org.

Scientific equipment
BD FACS Symphony A5.2 analyzers Photo by Robert Hood / Fred Hutch News Service

Flow Cytometry expansion and equipment update

February 2021

The Flow Cytometry shared resource has expanded to a second location in the historic Seattle Steam Plant. While the expansion was primarily to support the scientists in the building, the instrumentation there is available for anyone to use. The facility is in the northwest corner of the first floor. Please contact this location at 206.667.1221. The instrumentation at this location includes:

  • Two new Becton Dickinson SORP FACS Celesta analyzers (four lasers, 16 colors)
  • Two new BD FACS Symphony A5.2 analyzers (five lasers, 50 detectors), spectral or traditional
  • One new BD Symphony S6 sorter (five lasers, 50 detectors), spectral or traditional
  • One new Sony MA900 cell sorter (four lasers, 12 colors) 
  • One relocated Sony MA900 cell sorter (four lasers, 12 colors) 
  • One relocated CyTOF Helios 
  • One new Sony ID7000 cell analyzer (seven lasers, 188 detectors) 

The expansion of the core will allow more opportunities to schedule equipment and more convenience for the end user. Both locations have similar instrument capabilities. If you have direct questions, reach out to flowcytometry@fredhutch.org.

Data output from Sony ID7000
Data output from Sony ID7000 Image courtesy of the Flow Cytometry shared resource

Flow Cytometry receives Sony ID7000 

February 2021

The Flow Cytometry shared resource received the Sony ID7000, one of the first placements in the world. The instrument is equipped with six lasers (deep UV laser to be added this summer) and 150 fluorescence channel detection (soon to be 186 channel). The ID7000 utilizes the full spectrum of a fluorescent marker, collecting continuous fluorochrome emission from 360nm-920nm. The fluorescent spectra from colors with similar peak emission can now be detected by looking at total light fingerprint of each color, then applying an unmixing algorithm to resolve them. Building a panel with 40+ colors is now attainable using commonly available, directly conjugated antibodies. While the spectral data looks different, when it is unmixed and displayed in 2D format, it looks like normal flow data. This instrument is placed in the Steam Plant facility. If you are interested in this new technology and how it might fit in to your project, please call the Steam Plant lab at 206.667.1221 or email the team at flowcytometry@fredhutch.org.

Dail at 4

Coronavirus (COVID-19) Updates

Jan. 22, 2021

Fred Hutch, including Shared Resources, dialed up to level 4A (4A: full labs + ≤25% office-based researchers). Employees and visitors are required to follow the center’s guidelines put in place by the Incident Command team led by the Fred Hutch leadership that includes the latest guidance from public health officials in Seattle, King County, the Washington state Department of Health, the U.S. Centers for Disease Control and Prevention and the World Health Organization. Reach out to the specific Shared Resources core that you intend to access for additional guidance.