We analyse all types of high-throughput sequencing data from RNA-seq and single cell RNA-seq to variant sequencing (exome or whole genome), to ChIP-seq or bisulfite sequencing. With spatial profiling methods becoming more accessible, we have developed new workflows for spatial transcriptomic analysis and multimodal integration. We offer a dedicated bioinformatics training program for researchers interested in learning basic data skills and the analysis of high-throughput sequencing data. Our workshops focus on utilizing best practices in the field and research reproducibility.

Core provides in vitro HIV-1 neutralizing antibody assay services. Serves as resource for assessing breadth and potency of HIV-1 neutralizing antibodies, and for characterizing neutralization phenotype of HIV-1 isolates. Investigators send monoclonal antibodies or serum samples from vaccinated or HIV-1-infected individuals to the core for in vitro testing using the validated TZM.bl neutralizing antibody assay. The core also has the capability to phenotype primary HIV-1 isolates for sensitivity to broadly neutralizing antibodies. GCLP-compliant, In vitro testing of monoclonal antibodies or seurm samples, Validated TZM.bl neutralizing antibody assay, Phenotoyping of primary HIV-1 isolates.

The Harvard Center for Biological Imaging was opened May 17, 2010 and is one of the most innovative biological imaging centers in the world. In order to ensure investigators always have access to the latest and best technologies, the HCBI was designed to be an “Evergreen” microscopy facility. Imaging systems at the HCBI are leased rather than purchased and replaced every 2-3 years. This ensures that the facility remains relevant and is never in possession of outdated equipment. Currently, the HCBI contains 20 microscopes and 12 high-end processing stations including confocal, super-resolution, multi-photon, lightsheet, live cell imaging, high-content screening, slide scanning, spatial transcriptomics, laser dissection and macroscopy. The facility also features wet lab space, eukaryotic and prokaryotic incubation, and access to nearby animal care facilities for a wide range of species.

Our goal is to advance research efforts in the life sciences that cannot readily be accomplished in the traditional academic laboratory because of a need for expensive instrumentation or automation, scientific or organizational infrastructure, or multidisciplinary expertise.

To promote cutting-edge research and to foster scientific collaborations, we make our extensive resources available to scientists at Harvard. Our technical staff provide expertise and hands-on training and the use of instrumentation for a nominal fee. Researchers can sign up to use the instrumentation through an on-line scheduling system and conduct their experiments independently.

Proteomics and Mass Spectrometry Services, Quantitative Proteomics, LCMSMS, HPLC, C-terminal analysis, SILAC, FASP, MudPIT, GeLC, TMT quantitation and PTM analysis.

Offers advanced instrumentation and expert support to advance understanding of brain function and brain disease by providing researchers with access to cutting-edge technologies. Provides access to advanced instrumentation for optical microscopy, genomics, metabolic imaging and other technologies, as well as image analysis software. Provides expert support and training, data quality and interpretation.

-About the Core-

The BPF NGS Genomics Core Facility, formerly known as "The Biopolymers Facility," is a non-profit specialized service facility within the Department of Genetics at Harvard Medical School. The primary client base of the BPF consists of investigators at Harvard Medical School and affiliated research hospitals. While the majority of our users are located within the Longwood Medical Area, we also serve laboratories at schools, universities, and biotechnology companies globally.

Our mission is to provide investigators with access to technology services that will accelerate their research programs while simultaneously conserving time and resources by outsourcing laboratory experiments. Additionally, we offer a comprehensive range of popular reagents and supplies for immediate pickup from our Core Stock Room or Self-Service Supply Center. The core also provides cost-effective synthetic oligonucleotides and related products that are shipped directly to your laboratory through our IDT Portal. These resources facilitate the rapid development of research ideas into experiments while simultaneously reducing research expenditures through bulk pricing agreements and minimal, or no, shipping charges. We prioritize delivering high-quality data and expediting sample turnaround times.

Our comprehensive services encompass DNA and RNA Quality Assessment, Automation Services, Sanger DNA Sequencing, Next-Generation Library Preparation and Next-Generation Sequencing, Oligonucleotide Ordering, Reagent and Supplies Ordering, and training and access to a range of self-service instruments. We employ a comprehensive web-based Laboratory Information Management System (LIMS) to streamline ordering processes, monitor experiment progress, facilitate supply retrieval, grant data access, and facilitate invoice review and retrieval.

As a non-profit academic laboratory, we prioritize providing direct communication with our users regarding the processing of their samples. Our competitive pricing structure ensures that grant funds are allocated judiciously, aligning with the cost of experiments.

We offer complimentary consultations to facilitate discussions on collaboration opportunities, provide letters of support for funding proposals, and address inquiries about experimental design and the appropriate technologies and services to meet research requirements. Please do not hesitate to contact us at info@genome.med.harvard.edu for any inquiries.

Facility is small molecule and functional genomics high-throughput screening laboratory. It is built around modular work stations and most assays are performed in 384-well plates. There are over 500,000 small molecules available for screening at ICCB-Longwood and compound collection is continuously growing. Whole human and mouse genome siRNA libraries, arrayed sgRNA libraries, lncRNA siRNA libraries, as well as miRNA mimic and inhibitor libraries, are also available for screening. These libraries can be screened at the genome level or in focused subsets.

The HMS Electron Microscopy Facility makes high quality electron microscopy services, instrumentation and training easily accessible to all researchers. Our services include consultation and experimental design for a wide variety of biological samples for both SEM and TEM.

Open access light microscopy and tissue core located within Neurobiology Department.
Provides services in optical imaging, tissue clearing, in situ hybridization as well as introduces new equipment and cutting technology to the basic science community. Provides expertise, equipment, services and learning opportunities to researchers in the greater Boston area.

Core specializes in single cell and spatial transcriptomics, and multiomics. Provides custom services, education, training and expertise in multiple high-throughput single cell technologies.

Core specializes in analysis of nascent transcriptome using PRO-seq and TT-seq NGS methods. Provides services allowing users to submit prepared cells and receive analyzed data. Offers free consultations to help with experimental design, answer questions, and discuss data analysis.

The Mouse Behavior Core (MBC) offers a wide range of mouse behavioral equipment and assays to test a motor, cognitive, and affective behaviors. Trained users have access to eight behavioral testing rooms and a procedure room. The MBC staff offers consultation, training, and guidance in execution and interpretation of assays.

The Harvard Cryo-Electron Microscopy Center for Structural Biology is a joint effort by Harvard Medical School, Dana-Farber Cancer Institute, Boston Children’s Hospital, and Massachusetts General Hospital to provide state-of-the-art cryo-EM instrumentation and expertise for the Harvard structural biology community. This user facility offers consultation and training by staff in specimen preparation, microscope operation, image acquisition, and data analysis.

The Center for Macromolecular Interactions (CMI) in the department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School provides scientific consultation, training and access to shared biophysical equipment for the characterization and analysis of macromolecules and their complexes.

The facility offers training and access to instruments to measure molecular interactions by Isothermal Titration Calorimetry (ITC), Surface Plasmon Resonance (SPR), Biolayer Interferometry (BLI), MicroScale Thermophoresis (MST).

The facility also offers select data collection services, training and access on instruments to assess protein quality and biophysical properties by Differential Scanning Fluorimetry (DSF), Circular Dichroism (CD), Analytical Size Exclusion Chromatography with Multi-Angle Light Scattering (SEC-MALS), Dynamic Light Scattering (DLS) and Mass Photometry (MP).

Using libraries developed in the lab of Andrew Kruse, the CMI is also offering yeast surface display nanobody selections services.

confocal/multiphoton microscopy/electron microscopy/image analysis

State-of-the-art resource for NMR that offers services in fragment-based screening and drug discovery, characterization and QC of biologics and biosimilar drugs, metabolomics, protein NMR, small molecule NMR, and NMR of natural products. The facility offers 400-700MHz systems, many with cryogenic probes. The staff is highly experienced and dedicated.

The Mouse Engineering Core was established in 1992 operating at the BWH, and is now located at Harvard Medical School. The Mouse Engineering Core provides services for the generation of transgenic and knockout mice using state-of-the-art facilities and equipment.

The Core has all of the equipment necessary for generation of transgenic mice including a Nikon Diaphot microscope equipped with Nomarski Optics and Narishige micromanipulators for microinjections, Nikon surgical microscopes for egg isolation and transfer, a sutter needle puller and a de Fonbrune microforge. The facility maintains mice necessary for egg donors, egg recipients, and vasectomized males.

ES cell culture services have been offered for 15 years. The core offers electroporation of targeting vectors into ES cells and provides investigators with DNA to identify ES cells carrying the desired recombination events; and ES cell expansion for microinjection into blastocysts.

The core\'s newest services include CRISPR injections, sperm and embryo cryopreservation, and reanimation with fresh or frozen sperm via IVF or the thawing and implanting embryos.

The Research Computing Core is a set of research computing services provided by the Department of Information Technology at Harvard Medical School. The facilities include a high performance computing environment, O2, computational storage, and other services that support biomedical research such as research software licensing. Our services are only available to Harvard Medical School, Harvard University, and HMS Affiliates https://hms.harvard.edu/about-hms/hms-affiliates.

The Microscopy Resources On the North Quad (MicRoN) facility is a light microscopy core established by the Departments of Genetics, Immunology and Microbiology, and it is open to all HMS researchers, including Affiliated hospitals. MicRoN is a non-traditional decentralized or "floating" microscopy core. We support a wide range of imaging modalities ranging from widefield, TIRF, spinning disk and single point scanning confocal, multiphoton, FLIM and supper-resolution. The 14 microscopes that currently make up the core are embedded within the Departments of Microbiology, Immunology, and Genetics, housed in five microscope rooms on five floors of NRB and HIM. We find that this model generates a greater interaction among trainees from the three departments and encourages a more collaborative environment. We are proud of working with the Departments of Genetics, Microbiology and Immunology and would love hearing from you!

Currently, we provide analysis of gene expression using the Affymetrix GeneChip platform. Services using the Illumina platform will be available soon. For more information go to the services section of our website. For both platforms users of the facility provide us with high quality samples and the Microarray Resource does the rest. We also offer analysis of RNA, DNA and Proteins using Agilent Bioanalyzer.

We offer the same services to researchers outside of Boston University on an available-resource basis.

All interested researchers are encouraged to contact the Microarray Resource to discuss potential projects or to ask any question about the use of microarrays. Dr. Alekseyev can provide advice on experimental design, RNA isolation methods, and just about any aspect of array hybridization. Dr. Lenburg can provide advice on experimental design and data analysis.

Please note that we were able to reduce our pricing starting 12/16/2010.

The Brandeis EM facility offers wide variety of preparation and visualization ranging from standard 2D EM methods to high resolution 3D cryo-EM.
Instruments, training and assisted use are available for Brandeis faculty, staff, and lab members, as well as members of the broader scientific community, including other academic institutions and for-profit organizations.

The LMCF houses 13 high-end light microscopes including point scanning and spinning disk confocals, Airyscan, 3D-STED super resolution, widefield and TIRF systems. We offer training, consultation and access to powerful analysis computers with licensed softwares. We are open to external users from both academia and industry at competitive rates.

The BioMicro Center is an integrated genomics/bioinformatics facility located at MIT. The core supports sample isolation, library preparation, short and long read sequencing, single cell and spatial analysis, bioinformatics, and data management.

We provide services and instrumentation for imaging and characterization of bio- and nanomaterials with a strong focus on biological sample preparation. Some instruments are available for independent use. We also provide full service TEM, cryoTEM, SEM/FIB and cryoSEM/FIB, cryoFluorscence, sample preparation and imaging. Additionally, we conduct CLEM and cryoCLEM workflows utilizing cryoFluorescence, cryoSEM and cryoFIB with a focus on bio samples. In some cases the endpoint imaging is in the SEM/FIB (2D or 3D volumeEM). In other instances samples are transferred to one of a selection of cryoTEMs. We also provide immunoEM. In addition to imaging services we provide training on instruments for independent user access to: SEM, TEM, rheometer, AFM, DLS, and Spectradyne (counting & sizing nanoparticles). Our instruments and services are available to both non-profit and for-profit entities.

Nanowell Cytometry platform is a shared resource housed in the Flow Cytometry Core that provides researchers access to single cell analysis technologies developed in the Love and Shalek Laboratories at the Koch Institute.

Seq-Well is a portable, low-cost platform for massively-parallel single-cell RNA-Seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semi-permeable membrane, enabling efficient cell lysis and transcript capture.

Additionally, the Core offers access to the following tools that enable single cell imaging and retrieval:

1) CellCelector, a tool which enables users to isolate single cells using an ultra-precise robotic micromanipulator. We also offer access to nanowell microplates which enable automated isolation of monoclonal and viable clones.

2) Incucyte S3 system that allows automatic image acquisition and analysis of cells in a physiologically relevant environment.

Preclinical I&T’s mission is to assist the biomedical research community in evaluating disease and therapy within a complete biological system in-vivo. To do so, we focus on the use of minimally invasive and humane tools, with a strong focus in visualization and computation. Pharmacokinetic, pharmacodynamic, toxicity and dosing estimations can be performed with a variety of Preclinical I&T’s multi-modal services and technologies such as:

Digital imaging study design
Execution of pilot studies and preclinical trials
Optical Imaging: Fluorescence and Bioluminescence
Positron Emission Tomography (PET)
Radiotheranostics (Radioligand Therapy)
Quantitative gamma counting
Micro Computerized X-ray Tomography (microCT)
Ultrasound and Photoacoustic Imaging (USPA)
Magnetic Resonance Imaging (MRI)
Cryo-Fluorescence Tomography (CFT)
Image analysis workstations
Specialized data and imaging analysis workflows and software tool development

For more details please refer to the facility’s website: https://preclinical-imaging.mit.edu and https://ki-sbc.mit.edu/preclinical-imaging-testing

Core offers automation and screening capabilities. Equipped with environmentally-controlled high-content microscopes, automated liquid handlers, plate washers and readers, and robotic platforms, HTS aims to accelerate experiments from small-scale assays to large screening campaigns.

The Histology Core at KI-MIT processes a large variety of large and small animal tissues for paraffin/frozen sectioning and IHC. We also work up a large variety of samples with drug delivery devices and soft tissue constructs.

This Core Facility provides MIT and Boston area researchers with technical expertise, training and access to sophisticated instrumentation, enabling and supporting the use of a wide range of flow cytometry techniques. This technology allows simultaneous multiparametric analysis of many thousands of cells per second, enabling trained researchers to rapidly analyze complex cell populations using benchtop analysis flow cytometers. High-speed assisted cell sorting services provide researchers with fast, objective and quantitative recording of fluorescent signals from individual cells combined with physical separation of cells of particular interest.

This shared resource of the MIT Koch Institute provides fee-for-service support to investigators who utilize cultured stem cells such as organoids or novel mouse models to study human diseases.

We provide a customizable set of service options to match the specific needs of each project, including consultative advice and troubleshooting, complete tissue culture and microinjection servces within our dedicated facilities or hands-on training to enable investigators to perform these experiments either at their own laboratory or within our facilities.

The Barbara K. Ostrom (1978) Bioinformatics & Computing Facility is a shared institutional resource providing KI investigators with support, assistance and training in a wide range of bioinformatics topics. The core also maintains a high performance computing resource offering many bioinformatics applications, substantial processing power and secure storage and provides support for desktop computing and poster printing. Access is available to all members of the MIT community, to the extent permitted by available capacity. In recognition of funding support, priority access is given to members of the Core’s sponsoring entities (Koch Institute, MIT Biology, MIT Biological Engineering and MIT Center for Environmental Health Science) and NCI-funded research projects. In special circumstances, access may be available to non-MIT users (details available on request from the Facility Director, Charlie Whittaker)

Fee-or-Service lab providing the following: "Next-gen" DNA/RNA sequencing; Sanger sequencing; small scale and multiple peptide synthesis; larger scale peptide synthesis; peptide cellulose array synthesis; MALDI-TOF mass spectrometry and HPLC analytical and preparative scale.

Core offers Flow and Laser Cytometry equipment and services including FACS Analysis and Cell Sorting, to the scientific community.

Core provides protein sequencing services including Next-Generation DNA Sequencing, Peptide Synthesis, Protein Sequencing, and Mass Spectrometry. Provides expert technical and analytical support.

The CPCT Genomics Core enables UMass Boston investigators and academic and industry collaborators to carry out basic and translational genomics research. The Core leverages cutting-edge technologies and next-generation sequencing capabilities for research and clinical applications. We help investigators and clinicians analyze samples, identify genetic variants contributing to disease risk, and reveal complex mechanisms involved in human disease.

The Core offers cost-effective massively parallel sequencing with the Illumina HiSeq 2500 (v4, 1TB enabled) and Illumina MiSeq platforms; 10X Genomics Chromium Single Cell Sequencing Platform; Nanostring nCounter Analysis System; next-generation sequencing library preparation from RNA and DNA, and nucleic acid quality assessments using Bioanalyzer, Tapestation, Nanodrop and Qubit assays. Additional instruments include a Biomek FXp automated workstation, and a QuantStudio 12K Flex Real-Time PCR System.

The Center for Personalized Cancer Therapy is a collaborative venture between the University of Massachusetts Boston and the Dana Farber/Harvard Cancer Center (DF/HCC) and funded by the Massachusetts Life Sciences Center.

One of UMass Lowell’s Core Research Facilities, the Next Generation Sequencing & Genomics Lab provides Next-Generation DNA & RNA sequencing services and technical expertise including NGS library prep, DNA and RNA quality assessment, Fluorometric quantification of DNA/RNA/Protein, DNA & RNA isolation, PCR/qPCR, Qubit fluorometry, gene expression and drug development studies. Consultative services are also available.

The Nanofabrication Lab features a state-of-the-art, 4,200 ft2 Class 100 clean room equipped with over 40 pieces of process and analytical instrumentation for complex research projects that require micro and nano scale fabrication.

The Thermal & Mechanical Properties Lab houses a complete thermal analysis suite and is part of the Core Research Facilities. In this lab, researchers are able to investigate the behavior of a material under stress and temperature change. Service level work and technical expertise are also provided.

The Nuclear Magnetic Resonance Spectroscopy Lab features a state-of-the-art JEOL 400 MHz NMR equipped with auto sampling and automatic tuning & matching. The instrument can perform temperature and kinetic studies as well as x-nuclei and 2D experiments. A part of the Core Research Facilities, self-use and service work are available.

The Microscopy Core Laboratory (MCL) offers a variety of micro-imaging and micro-analysis solutions by providing access to several photon-, scanned probe-, ion beam-, and electron beam-based imaging and analytical instruments, services, and technical expertise for the characterization of materials including nano-engineered materials, microelectronics, photonics, biomaterials, and others with applications in life sciences, drug discovery, environmental and energy research. Consultative services are also available.

Cellular Imaging Core facility is light microscopy core in Boston Children's Hospital's Neurobiology Program. The Core maintains systems for Widefield, confocal, multiphoton, and lightsheet light microscopy as well as sample preparation and image processes tools and technologies to assist the microscopy community of Boston Children's Hospital in addition to the surrounding greater Boston area. Core services and equipment are available to all upon request, contact core staff for access.

The overall objective of the Molecular Genetics Core Facility is to provide high quality, low cost genomic technology services and expertise in a timely, affordable manner. Services offered include:

Nanopore PromethION sequencing
Electronic optical mapping on Nabsys
Optical Genome mapping on Bionano Saphyr
NGS (Illumina-based)
Sanger Sequencing
Single cell analysis/RNAseq
Transcriptomic spatial profiling
Gene expression analysis
Droplet Digital PCR & qPCR
Microsatellite/fragment analysis
SNP genotyping
Chromosomal microarray analysis
Sample prep & QC
Project consultation
Bioinformatics support

contact us at MGCF@childrens.harvard.edu

MGH NGS Core offers sequencing, upstream library construction (bulk RNA/DNA, single-cell), and post-sequencing analysis.
As of 2025 the core uses Illumina NextSeq 2000 sequencers (and a MiSeq). Single-cell (fresh, frozen, FFPE) libraries (3' & 5' RNA-Seq, CITE-Seq, ATAC-Seq, Multiome, FLEX) are made with 10X Chromium X.

Biostatistics core serves the needs of the HIV/AIDS researchers within the Ragon Institute and its affiliates at Harvard, MGH, MIT and University of Kwazulu Natal, South Africa. Provides expertise in planning, conduct and analysis of research with goal of enhancing scientific quality of HIV-related research at the institute. Primary objective is to ensure that studies are well designed, correctly analyzed, clearly presented, and correctly interpreted.

Services provided include tissue preparation, embedding and sectioning for electron microscopy, use of electron microscope and photography of thin sections, immunogold staining for electron microscopy, preparation and incubation of samples (cells and tissues) for immunofluorescence microscopy, confocal microscopy and digital imaging.

The MGH CCIB DNA Core, founded in 1995, is a non-profit research core laboratory within the Center for Computational and Integrative Biology at Massachusetts General Hospital (Boston). It has a 25+ year track record of increasing research efficiency with trusted high-quality, cutting edge research services at competitive rates and of providing access to state-of-the-art instrumentation, methodologies and expertise.

Core facility provides access to technologies in flow cytometry analysis including spectral analysis, high throughput imaging analysis (Amnis) and fluorescence assisted particle sorting (FACS). Instrument training, experiment and panel design, scientific consultation and sample processing are available. Offers training on facility equipment.

The Broad Institute Imaging Platform (https://www.broadinstitute.org/imaging) helps users turn images into answers by offering assistance and training with open source image analysis tools, creating custom image analysis workflows, and even creating custom software for image analysis when needed. We are open to collaboration with academics, non-profits, and for-profit organizations.