The BIDMC Bioinformatics Core, a Unit of the Precision RNA Medicine Core, provides support for analysis. It supports the management, integration and contextual analysis of biological high-throughput data, provide training on tools, databases and best practice.

The Center provides investigators access to comprehensive interdisciplinary, translational, and clinically-oriented facilities for high-sensitivity and high-throughput proteomics services. The Center has over 20 years of experience in precision medicine and proteomics biomarker discovery in tissue and biological fluids. We are the only service provider in the Boston are for the exciting and most comprehensive, highly multiplex 11,000-protein SomaScan v5.0 assay. We provide assistance in study design, experimental execution, data analysis, and systems biology, while also serving as a forum for education, scientific interactions, and cross-fertilization in proteomics.

The Functional Genomics and Bioinformatics Core provides consultative, laboratory, and bioinformatic services for next generation sequencing (NGS)-based applications. The development of next generation sequencing (NGS) technologies have made it possible to address biological questions comprehensively and with less bias at a systems level. Taking advantage of these approaches can require specialized technical and analytical skills that may be out of reach or not worth the investment for individual laboratories. The goals of this Core are to provide better access to these methods in order to enhance and facilitate a deeper understanding of complex disease processes and how they can be diagnosed and treated.

The Core is located on the 7th floor of the Center for Life Sciences building in the Longwood Medical area (3 Blackfan Circle, CLS-728). While the majority of clients come from Boston area research communities, we also service customers around the country. Most clients are in the fields of metabolism, obesity, and diabetes, as NORC and DERC funding provide discounted fees, and represent the expertise of the co-drectors Evan Rosen and Linus Tsai, though we can and have performed services for a broad range of research areas.

Specifically, our core services include:
1) Pre- and post-experimental consultation to determine proper experimental approach, design, and interpretation
2) Standalone RNA preparation, RNA and DNA Bioanalyzer analyses, chromatin shearing/shear checks
3) Sample quality assessment of DNA and RNA using the BioAnalyzer and Qubit assays
4) Library preparation, sequencing, and analysis of transcriptomes (RNA-seq), cistromes (ChIP-seq), chromatin accessibility (ATAC-seq)
5) Standalone sequencing on NextSeq500
6) Multiplexed 10x Single Cell/Nucleus Library RNA-seq Droplet generation, Library Preparation
7) Basic data analysis: quality assessment and normalization, genomic alignment, differential expression/enrichment, functional enrichment analysis (overrepresentation and GSEA), sample clustering, and motif enrichment
8) Bespoke data analysis, including integration of complex ChIP-seq and RNA-seq data sets, single-cell sequencing analyses

The Delivery Unit offers training and services on the NanoAssemblr Spark, NanoAssemblr Ignite+, and Malvern Zetasizer for the purpose of synthesis and characterisation of Lipid Nanoparticles (LNPs). The Zetasizer is able to read zeta potential and size of particles, including exosomes, liposomes, and LNPs.

The Glycomics Core provides services, instrumentation and expertise in glycomics to BIDMC research groups, affiliated and non-affiliated institutions and corporate companies.

The services proposed by the Glycomics Core includes:

Glycan Microarrays
Glycan analysis by Mass Spectrometry
Distribution of specific reagents
Trainings
The work is done on a fee-for-service basis.

The National Center for Functional Glycomics (NCFG) is an outgrowth of the high successful Consortium for Functional Glycomics (CFG) funded by the NIGMS/NIH from 2001 to 2014. The CFG generated two types of glycan microarrays that are available as a fee-for-service and approved by the Steering Committee of the CFG. These are the CFG Glycan Microarray version 5.2, and the Microbial Glycan Microarray (MGM) (also previously termed the Pathogen Array). Dr. Cummings is the Chair of the CFG, a world-wide consortium of more than 600 Investigators whose research is funded in the area of glycobiology or related sciences.

The NCFG is devoted to understanding protein-glycan interactions and its major resources are developments of new glycan microarrays and other technologies to identify ligands recognized by glycan-binding proteins, antibodies, and microbes.

MicroRNA Screening

Our unit offers full service microRNA screening of bio specimens using Mirxes ID3EAL assays. This highly sensitive qPCR-based technology can simultaneously screen for up to 376 microRNAs.

We offer the following panels:
• ID3EAL™ PanoramiR Panel targets 376 miRNAs involved in signaling pathways or disease mechanism
• ID3EAL™ Cancer Panel targets 352 miRNAs commonly studied in cancer

ABOUT US: The mass spectrometry, metabolomics and proteomics core at Beth Israel Deaconess Medical Center was established in 2004 led by Dr. John Asara and continues to grow rapidly. We provide excellent proteomics, metabolomics and lipidomics services with low prices and fast turnaround times. We have cutting edge equipment operated at optimal sensitivity and work and publish with world class researchers. We also maintain an active internal cancer proteomics and metabolomics/lipidomics research program with collaborative efforts. Our expertise is in identifying and quantifying protein modifications and dynamic protein-protein interactions in addition to polar metabolomics profiling and 13C/15N metabolic flux analysis. We accept samples from anywhere in the world and look forward to helping you and progressing your research to the next level.

The Translational MRI Core of the BIDMC Department of Radiology provides state-of-the-art MRI capabilities for imaging human subjects and potentially large animals as part of research studies. The facility operates a GE Discovery MR750 3T whole-body scanner completely dedicated to research.

Located in the Ansin Building on BIDMC's East campus, the scanner is FDA cleared for clinical use. In addition to commercial tools for clinical imaging, it has proprietary software including pulse programming environments and reconstruction programs and customizable software and protocols for applications including functional and structural brain imaging, abdominal perfusion and diffusion, muscle functional imaging and spectroscopy are available to users.

We upgraded to the GE Discovery 3T MR750 in the winter of 2016. This new system includes state-of-the-art hardware and software. The scanner is equipped with an optically coupled radiofrequency system for improved signal-to-noise ratio and with high-duty-cycle 50 mT/m gradients at 200 T/m/s slew rate.

The 3T system has high-speed echo planar imaging capabilities. Support for fMRI acquisition and visual and auditory stimulus presentation, diffusion tensor imaging, spectroscopy, and high quality anatomic imaging is available. The system has specialized receiver coils for sensitive imaging of particular anatomy. Additional customized coils can be manufactured in our RF lab. The system also has full broadband capability for multinuclear MRI and MRS, including (F-19, C-13, P-31, and Na-23).

To achieve high homogeneity, the 3T MR750 system is equipped with high order resistive shimming coils as well as super-conducting shimming coils. Additionally, the scanner will use broadband transmission to permit multiple frequency excitation schemes, which are crucial for spectroscopy and multi-nuclear imaging experiments. The GE MR750 system uses Multi-Drive RF transmit, which will improve body imaging by reducing RF transmit non-uniformity and power deposition.

The system will include a 32-channel Head array coil, 16-channel Head Neck Spine array, 32-channel Body Array, 8-Channel Torso Array, Flex Coils in small, medium, and large, and will have the capability to use disposable probes for imaging the prostate, cervix, and colon. Our 3T system will continue to have capabilities for multinuclear MRI and MRS. Through our contract with GE, the system will be continuously updated with new features, hardware, and capability.

Our MRI Research Suite is equipped with a Medrad (Bayer) power injector for contrast administration and Medrad (Bayer) physiologic monitors. Subject monitoring within the magnet includes non-invasive measures of heart rate, blood pressure, pulse-oximetry, end tidal CO2 levels, and ECG recording.