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  Rachel Brody, MD, PhD at .

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.

The Core provides facilities for the processing and banking of various hematologic tissues. Blood samples may be stored as whole blood or processed to yield specific blood fractions. Downstream applications include cytokine/chemokine studies, mass spectrometry, various nucleic acid studies (sequencing, microassays, etc.), immunologic studies, stimulation assays and expression studies. Samples are processed in BSL II facilities utilizing sterile technique and may be coded and de-identified as per individual studies. Tissues are stored at -80C freezers or vapor phase liquid N2. All audit trails may be traced with our secure databases. Tissues/cells that may be collected include:

  • Whole Blood
  • Serum
  • Plasma
    • Anticoagulants of choice
  • Peripheral Blood Mononuclear Cells (PBMCs)
    • CPT Tubes (Becton-Dickinson)
    • Hypaque-Ficoll
  • Polynuclear Cells
  • Buffy Coats
  • Nucleic Acid Isolation
    • PaxGene (Becton-Dickinson)
      • RNA
      • DNA
    • Whole Blood Isolation

For more information, please email Maryann Huie, PhD ( or call at 212 241-2248

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.


  • Galileo CK4600 Tissue Microarray System: 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 Fran Avila or Alan Soto, or call them at 212-241-3539.

The Pathology CoRE provides a variety of immunostaining services, including immunohistochemistry and immunofluorescence using commercial antibodies. We perform both semi-automated and full-automated (Discovery Ultra staining platform, Roche). We also provide antibody characterization/titration/interpretation and imaging services, as well as rapid immunohistochemistry staining for laser capture microdissection.


Discovery Ultra (Roche): 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/ Monica Garcia-Barros or call 212-241-6050 or at 212-241-2148.

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


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 (Bright-Field)

The core uses a Hamamatsu NanoZoomer S210 Digital Slide Scanner to perform whole slide scanning services from whole tissue sections, tissue microarrays, cytology specimens, etc.

The scanner provides bright-field image capture at 20X and/or 40X magnification. The system includes NDP.view2 Viewing software.
If you have any questions regarding scanning service, please email or call  Alan Soto at 332-215-2965 or Monica Garcia-Barros at 212-241-2148.

IHC Imaging
The Biorepository and Pathology CoRE offers quick imaging of IHC stained slides using Nikon EclipseCi-L upright clinical microscope.

Nikon Eclipse Ci-L offers bright-field image capture at 4X, 10X, 20X, 40X and/or 60X magnification. If you have any questions regarding imaging service, please email Tin Htwe Thin/ Monica Garcia-Barros or call 212-241-6050 or at 212-241-2148.

HALO from Indica Labs - Image Analysis

The Pathology Core offers quantitative tissue image analysis using HALO® Image Analysis Platform (Indica Labs). The platform offers 5 different modules:

  • Cyto-Nuclear IHC detects biomarker localization either in the cytoplasmic or nuclear location within the cellular compartment
  • Multiplex IHC provides analysis of up to 5 chromogenic markers to their subcellular compartments, nucleus, cytoplasm or membrane
  • Tissue Classification instructs the algorithm to delineate tissue based on its type (tumor, stroma, etc.,)
  • Quantification of tumor and immune cell with spatial analysis for Nearest Neighbor, Infiltration and Proximity analysis for Immuno-Oncology
  • Immune Cell quantification and measurement on proximity of immune cells to the second stain
  • Serial Section stain analysis for analysis of all markers in a single image, and support for serially stained tissue sections or a single tissue section, which has stained, stripped and re-stained for multiple markers. 

If you have any questions regarding image analysis service, please contact Tin Htwe Thin ( ; 212-241-6050) and Monica Garcia-Barros ( ; 212-241-2148)

Molecular DNA/RNA Extraction

The Pathology CoRE provides DNA and RNA (total/miRNA) extraction including quantitation/ quality services from a variety of specimen sources including blood, buffy coat, platelets, plasma exosomes, PAXgene, frozen/fixed (FFPE) tissues prepared by micro-dissection (LMD) or macro-dissection (scroll/punch/whole or partial scrape off), swabs, spit cups, brushes, cytofluids, and more. Free consultation is available.


  • Qubit fluorometric quantitation (Thermo Scientific)
  • NanoDrop 2000 spectrophotometer (Thermo Scientific)
  • Maxwell RSC 48 and Maxwell RSC 16 automated nucleic acid purification system (Promega)
  • QIAvac Vacuum System (QIAGEN)
  • BeadBug 6 homogenization (Benchmark)
  • ThermoMixer C heating/cooling/mixing instrument (Eppendorf)
  • Centrifuges for microtubes and 15/50mL tubes (Eppendorf)
  • E-Gel EX 2% electrophoresis system

For more information, please email Yayoi Kinoshita, DMD or call her at 212-241-4414.

The Biorepository is responsible for collecting, storing, processing, and distribution of human tissue (fresh, frozen, FFPE) and body fluids (blood, urine, and cerebrospinal fluid)

Our mission is to provide high-quality annotated specimens with the potential to be linked (with appropriate IRB approval and patient consent) to clinical and pathological data.

Specimens are readily available for research and open to all investigators within the Mount Sinai Health System, as well as to outside investigators.

Samples can be collected from Mount Sinai Hospital and affiliates.


To request specimens from the Biorepository please contact Rachel Brody, MD PhD ( ; 212-241-0678; ext. 40678)

A project BRC# will be assigned provided the following criteria are elucidated and placed on file:

1.An abstract or specific aims that clearly describe the project for which you will use human tissues or fluid, including a detailed description of collection requirements; grant support information for your research program; assurance of institutional IRB approval, GCO fund number.

2.Completed forms acknowledging responsibility in understanding of and adherence to appropriate safety standards for the protection of yourself and others while handling human tissues; acknowledging that you will not further distribute the materials disbursed to you by the Biorepository

3.Agreement to provide specific acknowledgement to the Mount Sinai Biorepository in any publications or grants related to the use of the tissues you receive.