Instrumental - February 2023

A Rogel Cancer Center Shared Resources Newsletter

FEBRUARY 2023

A MESSAGE FROM DR. KELLER

Dear Rogel Cancer Center Members,

Welcome to another edition of Instrumental!

With the new year comes new opportunities to engage with you through the many activities and services supported by our Shared Resource (SR) facilities. We are kicking off 2023 with announcements of exciting new technologies and instrumentation available within several of our SRs.

For our Service Spotlight, we focus on our Cancer Data Science Shared Resource that provides bioinformatic and bioanalytic tools and expert personnel for Rogel members conducting clinical, translational, basic and population science research.

Finally, we thank the over 100 Rogel members who provided feedback to the 2022 Shared Resource survey and announce the four lucky winners of our Zingerman’s lunch raffle.

If you have questions or comments you would like to share with us, you don’t need to wait until the next survey, a virtual suggestion box is always available on our website.

Thank you for your time,

Evan T. Keller, D.V.M., Ph.D.

Associate Director for Shared Resources

Rogel Cancer Center

SERVICE SPOTLIGHT

Cancer Data Science Shared Resource

The Cancer Data Science (CDS) Shared Resource consists of highly trained quantitative scientists who assist with data analyses and help conceptualize and develop research projects and clinical trials. CDS personnel have both broad and deep expertise in Biostatistics, Bioinformatics, and Clinical Informatics. CDS personnel engage and collaborate with Rogel investigators on development, design, analysis, interpretation, and publication of cancer research projects. In this edition of Instrumental we explore the service offerings of CDS by answering some frequently asked questions.

How do I request statistical and/or grant proposal assistance?

Start by completing our Project Intake Form to provide us with an overview of your project including the type of project, a brief description, and the expected timeline. We will review your request and CDS leadership will assign the appropriate member of our team for your work.

Can I talk to someone before requesting formal assistance?

Absolutely! CDS hosts virtual office hours each Wednesday beginning at 12:30 p.m. Please complete this form to request an appointment. Specific inquiries can also be directed to Veera Baladandayuthapani, Ph.D., director of CDS; or Arvind Rao, Ph.D., director of bioinformatics.

When should I reach out for statistical advice?

Recommended timelines that would significantly facilitate our planning process are:

Advance notice of 1 month towards meeting abstracts
2-3 months towards manuscripts (biostatistical/bioinformatics analysis, figure preparation, etc.)
3-6 months for R01 submissions
6-9 months for program projects (e.g., SPOREs, P01s)

My project requires a quicker turnaround. Can you help me?

For projects requiring quicker turnarounds, these will be addressed on a case-by-case basis based on resource availability and study priority.

What support do you provide for clinical studies and those that utilize electronic medical records?

We collaborate with investigators on design of clinical research protocols and observational studies. We offer support for the review, monitoring and oversight of clinical and prevention research protocols. We also assist in searching electronic medical records for case finding and for planning and executing research as detailed on our services and capabilities webpage.

I have data science experience but want to further my skills. Do you offer seminars or coursework?

Upcoming CDS webinars and previous recordings can be found on our events page and are also advertised to members via Rogel newsletters and email communications.

Does CDS offer access to computing resources for labs conducting in-house analyses?

CDS offers a variety of resources including software, protocols, and computing support. Recently, a general purpose Partek Bioinformatics software suite was purchased to facilitate graphical pipeline development for standardized, collaborative, reproducible analyses.

NEWS AND UPDATES

Bigfoot Available at All Flow Locations

The Flow Cytometry Shared Resource (FLOW-SR) has installed a ThermoFisher Bigfoot Spectral Cell Sorter at their NCRC location (Building 20 W, Room 134D) replacing the MoFlo Astrios. With this addition, Bigfoot technology is now available at all three FLOW-SR locations across campus. Please visit the FLOW-SR MiCores page to schedule machine time or training. Additional questions for this and other FLOW-SR technologies can be directed to David Adams, managing director of the Flow Cytometry Core.

Advanced Photon Source Upgrade Project

Advanced Photo Source user operations at LS-CAT will be paused as of April 11, 2023 to accommodate the year-long storage ring installation and commissioning period. In preparation for this outage, the SDS-SR has established an in-house X-ray facility to support researchers requiring macromolecular crystallography. An Excillum MetalJet-D2+ 70kV, 250W X-ray source equipped with high flux optics and Eiger2 R 4M hybrid photon counting detector is available to be scheduled via the Center for Structural Biology MiCORES website. Limited access to synchrotron radiation at ESRF, DLS, NSLS II and SSRL has been secured in conjunction with LS-CAT. For synchrotron time, please contact Jennifer Soules. Any additional questions, please contact Jeanne Stuckey, Ph.D.

New Screening Technologies Available

The high-throughput screening capabilities of the SDS-SR now include DNA encoded library (DEL) technology. DEL enhances early-stage drug discovery efforts by allowing up to 7 billion compounds to be screened via a direct target binding assay in a single Eppendorf tube. Small molecules are conjugated to DNA strands which act as a barcode. DNA sequencing is then used to identify hits against protein targets. For additional information please contact Jennifer Soules.

Single Cell Spatial Analysis Offers Three New Services

The Single Cell Spatial Analysis Shared Resource is pleased to announce the addition of three new services. Our newest spatial transcriptomics platform, Curio Seeker, interrogates whole transcriptomes of frozen tissue at a 10-micron resolution. For single cell analysis we have two new kits from BioSkryb that utilize single cells sorted into 96-well plates. ResolveDNA’s whole genome amplification enables single nucleotide variant (SNV) analysis and copy number variation analysis (CNV) whereas ResolveOME provides a unified system for single-cell whole mRNA transcriptome and whole genome amplification sequencing analysis. Please contact advanced-genomics@umich.edu with any questions.

New Location for Small Animal Radiation Research Platform

The SARRP: Muriglo System is moving to 3744 Medical Science 2 in the coming weeks. The Small Animal Radiation Research Platform (SARRP) was previously housed in the ARF complex and has been available to Rogel Cancer Center users since 2019. This state-of-the-art instrument permits cone beam CT and bioluminescence-based image-guided conformal radiation therapy of small animals.

Benefits include:

Treatment planning and delivering doses of radiation to distinct areas utilizing 3D imaging
Obtaining dosimetry data for target and surrounding tissues in the beam path
Ability to create a 3D contour of implanted cell lines/tumors engineered to express bioluminescent enzymes and deliver radiation therapy

Pricing is $90/ hour (billed in half hour increments). To discuss capabilities or schedule service, please contact David Karnak, manager; or Meredith Morgan, Ph.D., director.

New Microscopy Equipment

The BRCF Microscopy Core (Rogel Cell and Tissue Imaging Shared Resource) has expanded the range of imaging systems available to Rogel Cancer Center members. The BSRB location now includes new microscopes including a Zeiss Lightsheet 7 and a Nikon Ti2. The Lightsheet 7 provides fast, gentle volumetric imaging of larger format live and fixed samples including live model organisms (zebrafish, drosophila, C. elegans, etc.) and fixed tissues cleared by a variety of methods including iDISCO and CLARITY. The Nikon Ti2 is a widefield microscope supporting several modalities including brightfield, multichannel fluorescence, phase contrast and differential interference contrast. It is fully motorized and boasts the speeds necessary to rapidly acquire tiled images of large tissue sections and entire well plates. For more information, please visit our website. The SR has also purchased a Zeiss 980 AiryScan confocal and super resolution microscope that will be installed at the BSRB in early April.

Decreased Turnaround Time & EM Methods Consultation

Through an increase in staffing, the Microscopy Core (Rogel Cell and Tissue Imaging Shared Resource) has decreased the turnaround time for most conventional TEM projects to 3-4 weeks. The facility is once again offering semi-thin sectioning with Toluidine blue staining. Please submit project requests through MiCores. Additionally, the core is looking for your input on what advanced EM methods would be most impactful to your research. If you have projects in mind using CLEM, FIB-SEM, array tomography, high pressure freezing / freeze substitution, immunostaining, or other advanced EM methods, please contact us at microscopy@umich.edu to schedule a consultation.

AWARDS

2022 Human Proteome Organization (HUPO) Award

Alexey Nesvizhskii, Ph.D., director, Proteomics Shared Resource, has received the Distinguished Achievement in Proteomic Sciences Award. The award was presented in recognition of the more than 20 years that he has dedicated to the creation of widely used algorithms and software tools that have enabled users worldwide to better interpret proteomics experiments.

Congratulations to Dr. Nesvizhskii on this significant accomplishment.

Zingerman's Raffle Winners

We thank all the Rogel members who took the time to provide their feedback to the 2022 Annual Shared Resource Survey. A perk of completing the survey was entry to a raffle to receive a Zingerman's lunch. Congratulations to the following members who will receive an e-gift card in their inbox following this announcement:

Christina Angeles, M.D., Cancer Hematopoiesis and Immunology
David Hanauer, M.D., Cancer Control and Population Sciences
Mukesh Nyati, Ph.D., Developmental Therapeutics
Thomas Wilson, M.D., Ph.D., Cancer Genetics

We want to hear your feedback!

Please submit your thoughts about our new internal emails here.

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