Services and Equipment

The Biorepository and Pathology CoRE is a multi-dimensional service group providing consultation and technical support for the translational and basic science groups across the Mount Sinai Health System. 

If you have any questions regarding these services, please contact Michael Donovan, MD, PhD by e-mail or at 212-241-4868.

Please note: it is important that you acknowledge the Biorepository and Pathology CoRE in all publications and grants that include data derived from our facility.

We offer basic histology services, including processing, embedding and sectioning of frozen and fixed (human and animal) tissue samples. We provide hematoxylin and eosin stained slides, as well as multiple special stains (e.g. Acid Fast Bacilli (AFB), Periodic Acid Shift (PAS), Giemsa, Gram, Masson’s trichrome etc...). We can generate unstained sections for a variety of applications, such as immunohistochemistry, in situ hybridization, laser capture microdissection, etc.). We also offer the generation of tissue microarrays (TMA) from different tissue blocks.

Equipment

  • Chemicon International ATA100 Tissue Array: Advanced EDM Automation Tissue Array High-throughput construction of customized tissue array. Involves multiple tissue samples extracted from donor paraffin-embedded tissue blocks into a single paraffin block.
  • Sakura E300 Tissue Processor: Automatically process tissue samples for embedding by dehydration after fixation in 10 percent Neutral Buffer Formalin
  • Sakura Tissue-Tek Embedding Center: Used to embed the processed tissue samples in paraffin
  • Leica Cryostat: To section frozen tissue blocks for further use in a variety of applications

If you have any questions regarding these services, please email Marlon J SuarezLisette Conde or Alan Soto, or call them at 212-241-7582.

The Pathology CoRE provides a variety of immunostaining services, including manual or automated (Ventana system, Roche) immunohistochemistry and immunofluorescence using both commercial and in-house antibodies. We also provide antibody characterization/titration/interpretation and imaging services, as well as rapid immunohistochemistry staining for laser capture microdissection. We perform both manual and automated (Ventana system, Roche) in situ (RNA / DNA) hybridization.

Equipment

  • Discovery Ultra: Automated Immunohistochemistry (IHC)/In situ hybridization (ISH) research slide staining system. For research application including IHC, multiplex Immunofluorescence, DNA / RNA ISH

If you have any questions regarding these services, please email Tin Htwe Thin or call 212-241-6050.

The Pathology CoRE provides laser capture microdissection services from frozen and or paraffin-embedded tissue samples as well as cells. We also offer training to all investigators to use the system. We can provide sectioning of samples onto special membrane-coated slides and rapid immunostaining as required.

Equipment

  • Leica Microsystems LMD6500 Laser Microdissection: For specimen collection by gravity contact, contamination-free to obtain ultra-pure sample of single cells, both from tissue samples and cells.

If you have any questions regarding these services, please email Tin Htwe Thin or call 212-241-6050.

Whole Slide Scanning and Image Analysis

The Pathology CoRE offers whole slide (digital) scanning and image analyses services using the Olympus microscope scanner and Visiopharm Integrator software, from both whole sections and tissue microarrays.

Equipment

  • Pannoramic 250 FLASH II (Digital Scanner): We have a Perkin Elmer Digital Slide Scanner with capacity for Bright Field or Immunofluorescent image capture at 20x and/or 40x magnification. Our system includes the Pannormaic Viewer for Image Analysis (Cell Quant and Pattern Quant) and Immunofluorescent filters (DAPI, FITC, CYC, CY5).
  • Olympus scanner with Visiopharn Integrator Software System: It provides a digital scanned image of both whole and TMA sections as well as automation image analysis of whole slide / TMA images. Visio Pharm Software: Quantitative assessment of H&E and immunostained regions to create quantitative biomarker features such as area and intensity.
  • Olympus confocal microscope, equipped with a variety of filters to evaluate different fluorescent probes.


If you have any questions regarding these services, please email Marlon J SuarezLisette Conde or Alan Soto, or call them at 212-241-7582.

The Pathology CoRE provides DNA and RNA/ miRNA extraction including quality/quantitation services from a variety of specimen sources including blood, buffy coat, frozen/fixed tissues, swabs, spit cups and brushes.

Equipment

  • NanoDrop 2000 spectrophotometer Thermo Scientific:  To assess DNA/RNA quality-quantity after extraction.

The Biorepository supports the procurement, storage and tracking of tissue samples and body fluids, from consented and deidentified collections. Researchers interested in collection activities should contact one of the biorepository pathologists for additional information. For all requests, please provide a detailed outline of the specific aims for your research project and the specific tissue / body fluid requirements (for some diagnoses, tissue / fluids can only be distributed as they become available). In addition, please provide: scientific rationale, anticipated techniques / assays using the specimens, number of specimens requested, type of preparation (fresh, frozen, RNAlater, formalin-fixed), and anticipated clinical information.

All specimens are retained anonymously, and patient specific (identifier) information is only released with appropriate, documented consent and written IRB approval.

Equipment

  • REVCO -80˚C upright freezer: Used to keep the frozen OCT tissue collection of the Biorepository.
  • Harris -80˚C upright freezer: Used to keep the frozen NUNC collection of tissue samples, body fluids, and RNA samples from the Biorepository.
  • Panasonic -80˚C chest freezer: Used to temporarily store samples being collected in the Biorepository prior to permanent storage.
  • Summit Refrigerator: Used to keep DNA samples from the Biorepository.
  • Thermo Scientific 4.3 liter LN portable tank: To snap-freeze the tissue samples in a NUNC vial.
  • Thermo Safe storage chest dry ice container: Used to store daily dry ice for the Biorepository use.

In order to evaluate your request, Biorepository personnel require that you provide the following information:

  1. Complete the Specimen Request form, and provide a list of approved grant support for your research program (i.e. federal grant number, foundation or other private support, and identify current collaboration or mentor-trainee affiliations), as well as assurance of your institution IRB approval, and a GCO fund number, as requested in the form.
  2. Provide an abstract or list of specific aims that clearly describe the project for which you will use human tissues or body fluids including a detailed explanation about the collection protocol you need.
  3. Read, sign and return the Human Specimen Handling Risks and Safety Precautions Statement. This will acknowledge your responsibility in understanding of and adherence to appropriate safety standards for the protection of yourself and other laboratory personnel under your supervision while handling human tissues / body fluids.
  4. Read, sign and return the Human Specimen Single User Agreement. This will acknowledge your responsibility in not distributing any portion of the tissue / body fluids to colleagues or other investigators, and that all such inquiries will be directed to the Biorepository personnel.
  5. Read, sign and return the Biorepository Acknowledgment Agreement. This will indicate that you have agreed to provide specific acknowledgement of the MSB in any publications related to the use of these tissues / body fluids.

All requests will be reviewed in the order which they are received. You will be notified regarding the status of the request and if approved, when specimens are available for pick-up in the Department of Pathology. You will be assigned a project number (BRC ID), which needs to be used in all communications with Biorepository personnel regarding this specific project.