Boston Functional Genomics and Bioinformatics Core

Overview

The Functional Genomics and Bioinformatics Core offers a wide range of Next Generation Sequencing (NGS) technologies and associated bioinformatic analyses to members of the BNORC and Boston area community. This “soup to nuts” approach enables users to go from raw samples to publication-quality figures in one place.

Services

Our services can be broadly divided into 3 categories: Consultation, Data Generation, and Data Analysis.

Consultation

One of the most important services that the Core provides is pre-experimental consultation. Many investigators know that they want to take advantage of these powerful new tools, but they don’t have the expertise to frame their questions in such a way that matches available techniques. This is a key point: many NGS services are available as send-out services or even as kits that can be purchased directly from vendors and performed in the users’ own laboratories. In our experience, however, the average biomedical scientist is intimidated by the complexity of these techniques. Our Core Directors, technicians, and bioinformaticians have detailed knowledge and hard-won, real-world experience of the pros and cons of available approaches, and the specific challenges of applying these techniques in tissues and cell types relevant to BNORC users.

During consultations, we seek to define and frame experimental questions, then suggest an appropriate experimental approach, taking into account the time, budgetary, or personnel constraints of individual users. The Co-Directors have expertise in the application of each of the core methodologies offered to scientific questions of metabolic relevance and can help users avoid many of the pitfalls that can be encountered, before the commitment of significant time, energy, or money. Of note, in approximately 1/3 of our consultations, we guide users to the conclusion that they do not, in fact, need our services.

Data Generation

n the wet lab, samples are provided by the user in any of a variety of forms, usually frozen tissue, isolated cells, purified RNA or chromatin. Our technical staff then prepare the samples as required using standard operating procedures (SOPs) developed in the Core, and generate libraries. Proper QC is performed at each step along the way. We offer:

• Sample quality assessment of DNA and RNA using the BioAnalyzer and Qubit assays
• Library preparation, sequencing, and analysis of transcriptomes (RNA-seq, including low-input), cistromes (ChIP-seq), chromatin accessibility (ATAC-seq)
• Single Cell/Nucleus isolation, droplet generation and library preparation for RNA-seq, ATAC-seq
• Standalone RNA preparation, RNA and DNA Bioanalyzer analyses, chromatin shearing/shear checks
• Standalone sequencing on NextSeq500

Data Analysis

Each distinct project is assigned to an individual bioinformatician for consistency across that project. For data generated in-house, all data is processed through in-house pipelines that adapt widely-used analysis software (e.g., edgeR, Seurat, CellRanger, CellBender) to provide best practices, high quality, interfaceable data back to the user, including standard PCA, mean-difference, and volcano plots, pathway analysis, and formatted data that can be easily loaded onto platforms such as the Broad Single Cell Portal or Morpheus matrix visualization and analysis. We also provide customized analysis of NGS data, specializing in integration between genetic, transcriptional, and epigenetic datasets.

Equipment