Core Scientist: José Ordovas-Montanes, PhD
Instruments
- Visium 10x Genomics Chromium
- LeviCell 1.0 cell isolator – scRNAseq – paramagnetic cell isolation with very low levels of cell damage or perturbation
- Agilent 4200 TapeStation System – automated electrophoresis tool for DNA and RNA sample quality control
Fees
| Instrument | HDDC Member | BCH Non-Member | Non-BCH Non-Member | Industry |
| 10x Chromium | $115/hr | $115/hr | $149.50/hr | $258.75/hr |
| LeviCell Isolator | $50/hr | $50/hr | $50/hr | $50/hr |
| Agilent TapeStation | $14/hr | $15/hr | $20/hr | $36/hr |
Consultation & Training
scRNA-seq and Bioinformatics: In depth expert consultation, training, and real-time guidance for HDDC members pursuing single cell transcriptomic experimental approaches are provided by Core Scientists José Ordovas-Montanes, PhD and Marc Elosua Bayes, PhD (who also form the scientific leadership of the Cell Discovery Network located at Boston Children’s Hospital). The Network/HDDC collaboration provides in person guidance and training via: 1) Office hours 3 days a week, 2) Quarterly 2-day interactive training workshops, 3) Bi-weekly discussion groups, and 4) Monthly resource updates on their GitHub repository.
Main points of training and consultation/guidance provided focuses on: 1) Experimental design in single-cell, 2) How to access and move data, 3) How to access publicly available datasets, 4) Running 10X CellRanger on E2, 5) Explaining file outputs from various sequencing pipeline steps, 6) How to interpret quality control, 7) Normalization of data, 8) Integration, 9) Building reference genomes with exogenous sequences (viruses, fluorescence, etc), 10) Gene module analysis, 11) Differential expression, and 12) Differential composition.
HMS Single Cell Core (Mandovi Chatterjee, PhD, Director): Provides guidance for tissue preparation, reagent design, reagent/oligo synthesis and validation, and experimental design as noted above. The Core can also provide full service for spatial transcriptomic imaging and slide-seq and stereo-seq.
Core C aims to support between 10-20% of cost for members use of these collaborating institutional Cores.