The Biorepository and Pathology CoRE processes various hematologic tissues and other liquid biospecimens. Samples may be stored as whole blood or processed to yield specific blood fractions. Downstream applications may include cytokine/chemokine studies, mass spectrometry, various nucleic acid studies (sequencing, microassays, etc.), immunologic studies, stimulation assays, and expression studies.

Our samples are processed in BSL-2 facilities utilizing sterile techniques and may be coded and de-identified. Tissues are stored in -80C freezers or in the vapor phase of liquid N2. All audit trails may be traced with our secure databases. Tissues and cells that may be collected include whole blood, serum, plasma, peripheral blood mononuclear cells, polynuclear cells, buffy coats, and may subsequently undergo nucleic acid isolation. 

For more information, contact Maryann Huie, PhD.                                           

The CoRE offers 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, periodic acid-Schiff, Giemsa, Gram, Masson’s trichrome, etc.). We also generate unstained sections for various applications, such as immunohistochemistry, in situ hybridization, and laser capture microdissection. And, we can create tissue microarrays.

Equipment for these services include:

• Galileo CK4600 Tissue Microarray System. Advanced EDM Automation Tissue Array with 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 processes tissue samples for embedding by dehydration after fixation in 10 percent Neutral Buffer Formalin.
• Sakura Tissue-Tek Embedding Center. Embeds the processed tissue samples in paraffin.
• Leica Cryostat. For sectioning frozen tissue blocks for further use in a variety of applications.

For more information, contact Alan Soto and Shawn El Naggar.

We provide a range of immunostaining services, including immunohistochemistry and immunofluorescence using commercial antibodies. We perform both semi-automated and fully-automated immunostaining using the Discovery Ultra staining platform, from Roche. We also provide antibody characterization/titration/interpretation and imaging services, as well as rapid immunohistochemistry staining for laser capture microdissection.

Equipment for these services includes the Discovery Ultra (Roche), which is an automated immunohistochemistry/in situ hybridization research slide staining system for research applications including IHC, multiplex Immunofluorescence, DNA / RNA ISH.

For more information, contact Tin Htwe Thin or Monica Garcia-Barros, PhD.

The CoRE offers laser capture microdissection service from frozen and/or paraffin-embedded tissue samples, as well as cells, along with training to all investigators interested in using the system. We also section of samples onto special membrane-coated slides and perform rapid immunostaining as needed.

Equipment for this service includes Leica Microsystems LMD6500 Laser Microdissection for specimen collection by gravity contact, contamination-free, to obtain ultra-pure sample of single cells, both from tissue sections and cells.

For more information, contact Tin Htwe Thin.

Whole slide scanning services are available through the Biorepository and Pathology CoRE.

Whole Slide Scanning (Bright-Field). The CoRE uses a Hamamatsu NanoZoomer S210 Digital Slide Scanner to perform whole slide scanning services for whole tissue sections, tissue microarrays, cytology specimens, etc. The scanner provides bright-field image capture at 20X and/or 40X magnification, and the system includes NDP.view2 viewing software. For more information, contact Alan Soto or Monica Garcia-Barros, PhD.

IHC Imaging. The Biorepository and Pathology CoRE offers quick imaging of IHC stained slides using a Nikon Eclipse Ci-L upright clinical microscope. Nikon Eclipse Ci-L offers bright-field image viewing at 4X, 10X, 20X, 40X and/or 60X magnification. For more information, contact Tin Htwe Thin, PhD or Monica Garcia-Barros, PhD.

HALO from Indica Labs - Image Analysis. The Biorepository and Pathology CoRE offers quantitative tissue image analysis using the HALO® Image Analysis Platform (Indica Labs), which provides multiple modules with different functions:

• Cyto-Nuclear IHC. Detects biomarker localization either in the cytoplasmic or nuclear location within the cellular compartment
• Multiplex IHC. Quantifies expression of up to 5 chromogenic markers to their subcellular compartments, nucleus, cytoplasm or membrane
• Highplex FL. Quantifies expression of an unlimited number of fluorescent biomarkers in any cellular compartment (membrane, nucleus and cytoplasm)
• Tissue Classification. Instructs the algorithm to delineate tissue based on its type (tumor, stroma, etc.)
• Immune Cell.Quantification and measurement on proximity of immune cells to the second stain
• Serial Section. Analyzes serial tissue sections with different markers or a single tissue section which has been stained, stripped, and re-stained for multiple markers. Brightfield images are deconvolved into their composite stains and converted to pseudo-fluorescent images before subsequent registration. Fluorescent images can also be registered. The registered serial images can be fused into a single composite fluorescent image that can be analyze using Highplex FL.
• Area Quantification. Deconvolves up to five colors in brightfield and measures positive area and average optical density for each stain and stain colocalization
• Area Quantification FL. Measures the positive area, average intensity and dye colocalization of an unlimited number of fluorescent dyes
• Spatial Analysis. Plots cells and objects from one or more images and performs nearest neighbor analysis, proximity analysis, and tumor infiltration analysis
• Simultaneously analyzes up to three chromogenic and/or silver-labelled DNA or RNA ISH probes on a cell –by-cell basis, measuring numbers and area per cell and compartment, and calculates H-scores for each probe

HALO AI®

• HALO AI. Based on deep learning networks, Halo AI provides a collection of segmentation, classification and phenotyping tools for brightfield and fluorescent applications.
  • Tissues Segmentation. Trains AI-based MiniNet and DenseNet networks to classify tissue into user-defined classes.
  • Nuclear Segmentation. Chooses between trainable AI-based nuclear segmentation networks to optimize segmentation accuracy when nuclear morphologies vary.
  • Membrane Segmentation.Trains AI-powered membrane segmentation networks to accurately delineate cell membranes for specific assays.
  • Cell & Object Phenotyping. Trains a phenotyper to quantify cell types or objects of interest.

For more information, contact Tin Htwe Thin, PhD or Monica Garcia-Barros, PhD

The Biorepository and Pathology CoRE provides DNA and RNA (total/miRNA) extraction for next generation sequencing or spatial transcriptomics.  We can extract DNA and RNA from a variety of specimen sources, including blood, buffy coat, platelets, plasma exosomes, paxgene tubes, frozen/fixed tissues prepared by micro-dissection or macro-dissection (scroll/punch/whole or partial scrape off), swabs, spit cups, brushes, cytofluids, and more. (A free consultation is also available.)

Equipment for extraction services include:

• TapeStation 4200 automated electrophoresis system (Agilent)
• 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, contact Yayoi Kinoshita, DMD.

The Biorepository is responsible for collecting, storing, processing, and distributing 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 approval and patient consent) to clinical and pathological data.

Our specimens are available for research and open to all investigators within the Mount Sinai Health System, as well as to outside investigators. Samples may be collected from Mount Sinai Hospital and affiliates. To request specimens from the Biorepository, contact Rachel Brody, MD PhD.

A project BRC# will be assigned when these are submitted and approved.

• A brief description that clearly describes 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 Review Board approval, including GCO fund number.
• Completed forms that acknowledge responsibility in understanding of and adherence to appropriate safety standards for the protection of yourself and others while handling human tissues; acknowledgment that you will not further distribute the materials disbursed to you by the Biorepository.
• Agreement to provide specific acknowledgement to the Mount Sinai Biorepository in any publications or grants related to the use of the tissues and services you receive.