Core Scientist: José Ordovas-Montanes, PhD
Equipment
- Vizgen MerFISH Scope – spatial transcriptomics (200 nm resolution)
- Visium 10x Genomics CytAssist – spatial transcriptomics (2µm resolution)
- Supplementary instrumentation available through the HMS Single Cell Core includes: Vizgen MerFISH Scope, Visium 10x Genomics CytAssist, and Visium 10x Genomics Chromium
Fees
| Instrument | HDDC Member | BCH Non-Member | Non-BCH Non-Member | Industry |
| Vizgen MerFISH Scope | $9.80/hr | $9.80/hr | $12.65/hr | $22/hr |
| 10x CytAssist | $100/hr | $100/hr | $135/hr | $250/hr |
Consultation & Training
Spatial Transcriptomics: HDDC Core Scientists (José Ordovas-Montanes, PhD and Marc Elosua Bayes, PhD) will consult directly and/or orchestrate referrals for HDDC members to the Harvard Medical School Single Cell Core (Directed by Mandovi Chatterjee and Pratyusha Bala in Spatial Transcriptomics – with Jeff Moffitt, PhD, Scientific Advisor) for consultation and hands-on guidance for studies involving spatial transcriptomics using Vizgen MerFISH Scope technologies. The HMS Single Cell Core will provide guidance for tissue preparation, reagent design, synthesis and validation, and experimental design. Imaging by Vizgen MerFISH Scope at 200nm resolution is provided by HDDC Core C, with back up access to a second Scope located in the Harvard Single Cell Core if access is problematic. Dr. Jeff Moffitt, PhD will provide consultation and guidance on all aspects of spatial transcriptomics where needed. Dr. Moffitt helped originate this technology.
The Core also provides guidance, training, and equipment for spatial transcriptomics using the Visium 10x Genomics Platform with CytAssist – instruments contained within HDDC Core C. This provides 2µm resolution.
Bioinformatics: In depth expert consultation and real-time guidance on analysis and publication of scRNAseq and spatial transcriptomic studies for HDDC members is provided by Core Scientists (Ordovas-Montanes PhD and Marc Elosua Bayes, PhD) or via collaboration with the Harvard Single Cell Core respectively – as described above. Full service bioinformatic support through publication is provided by collaboration with the Bioinformatics Core at Boston Children’s Hospital. The BCH Bioinformatics Core (Piotr Sliz, MD, PhD and Shira Rockowitz, PhD, Directors) provides both help or full service with experimental design, data collection, analysis, and integration and visualization for any kind of biomedical research. The Core provides consulting, software, tools, training and best practices. Services provided can range from transcriptomics projects using single-cell RNA sequencing and analysis across multiple timepoints to genomics, proteomics, metabolomics and epigenomics analyses and integrations. Eight full-time biostatisticians are available to serve HDDC members referred to the core after initial uptake and consultation with Drs. Ordovas-Montanes and Bayes.
Core C aims to support between 10-20% of cost for members use of these collaborating institutional Cores.