Past Newsletters: September 2023
February 2024
Welcome Dr. Jennifer Hong to the CQB
Dr. Hong joined the CQB as a Project Leader in October 2023. Her project “Understanding brain extracellular matrix in the tumor microenvironment” seeks to better understand seizure onset in patients with brain tumors, by performing digital spatial profiling (DSP), and Visium 10x Single-nuclei RNA sequencing on brain tumor specimens to evaluate PNN structure and composition in the TME. The project will then apply machine-learning approaches to analyze these high-dimensional data in order to identify PNN features that relate to a clinical history of seizures. Her group will test the hypothesis that tumor-related PNN degradation in patients is associated with severe neurologic symptoms. It will also result in major development of novel histologic and computational techniques for evaluation of PNN structure and function that can be broadly applied to other, similarly complex biomedical datasets.
Dr. Hong will be presenting “Understanding the Brain Tumor Microenvironment” at Dartmouth Cancer Center Grand Rounds, February 20th in Auditorium E from 12-1pm.
Charles Hood Foundation awards Morhardt Lab with Childhood Health Award
Drs. Morhardt, Kolling, and Wilkins
The Morhardt Lab has received funding from the Charles Hood Foundation to study environmental chemical implications on genitourinary system development in zebrafish. This work was driven by preliminary genomic data developed through the CQB with the help of Fred Kolling IV and Owen Wilkins. The award runs over two years, and the Morhardt Lab proposal was selected from a competitive field.
Updates from the Single Cell Genomics Core
The SCGC has had a steady increase in the number of users since it was established in 2019. Though CQB affiliates do make use of the SCGC core services, the majority of users are from elsewhere within Dartmouth College and the Cancer Center.
Number of users by year and service utilization during 2023
New Equipment: 10x Genomics Xenium
With a standard 11mm x 22mm slide capture area, cassette-based reagent addition for higher throughput, and 50nM resolution to detect in situ individual transcripts, our new 10x Genomics Xenium comes with many advantages. It offers a non-destructive workflow which allows you to follow-up with Post-Xenium H&E, IF, or IHC on the same slides, 2-day sample prep, long reagent shelf life, streamlined data management, sophisticated analysis software with 3rd party integration, and predesigned panels human and mouse including brain, pan-cancer, colon, breast, and lung.
10x Genomics Seminar
The Genomics and Molecular Biology Shared Resource and CQB COBRE Single Cell Genomics Core are excited to host 10x Genomics for a seminar on February 22nd, 2-3pm in DHMC Auditorium E, with an additional 30 minutes available after the seminar to speak with the 10x team*. The talk will focus on our newly installed Xenium platform which generates spatial transcriptomics data at 50uM resolution for up to 500 targets in both fresh frozen and FFPE tissue sections. Light refreshments will be served. Register Here
*We will be announcing a grant program to accelerate Xenium data generation for a small number of projects at the seminar.
Updates from the Genomic Data Science Core (formerly Data Analytics Core)
The Genomics Data Science Core (GDSC) had over 80 jobs in 2023, mostly for members of Dartmouth College and the Cancer Center.
GDSC has developed a number of pipelines to offer faster and more consistent services. The newest additions are underlined.
- Transcriptomics: RNA-seq, Single cell RNA-seq, smRNA-seq, Single cell Multiome, Spatial omics – Visium
- Epigenomics: ATAC-seq, Single cell ATAC-seq, ChiP-seq, CUT&RUN, De novo modification detection
- Genome: Assembly, variant calling, Metagenomics, TCR-seq
- Workflows in development: Spatial omics – Xenium
COBRE supplement: Feasibility of leveraging Cloud Compute systems for Data Reduction
With their latest Cloud Computing supplement, Shannon Soucy & Tim Sullivan are examining the feasibility of using cloud compute systems as opposed to on-site computing resources.
Upcoming EAC Meeting
We will be gathering in April to meet with our External Advisory Committee (EAC). Our cores will share updates, project leaders will present on the progress of their projects, CQB member labs poster session, and researchers will have a chance to discuss their work in person with our EAC.
Update on Our Phase II Funding
We are happy to report that our Phase II grant submission received a fundable score and we have submitted our Just in Time! Thank you everyone who assisted with our grant proposal, and everyone who has helped make our Center a success!
CQB Travel Awards
The Center for Quantitative Biology (CQB) is pleased to offer travel awards designed to provide an opportunity to present research, engage with other researchers, learn new methods, etc.. Intended for senior PhD students (post-qualifying exam) or a post-doctoral fellows in CQB member labs who wish to present at a conference or participate in a course, the award will cover up to $1200 to be used for registration, lodging, airfare, ground transportation, meals, or a combination thereof.
Learn more and apply HERE.
Other Funding Opportunities
We fund selected pilot research projects through our Pilot Program and continue to offer event support funding.
Got news to share?
Do you have an open position in your lab? Anyone in particular deserve a shoutout? Have you received a grant recently? Published a paper you would like us to highlight? We would love to share your news in the next edition of our newsletter! Submit your entries anytime.
Please CITE US! CQB COBRE grant from NIGMS (P20GM130454). Visit our website for more information on citing the grant.