Human Immune Monitoring
The Human Immune Monitoring Core (HIMC) provides top-quality, cost-effective services for deep, comprehensive, multi-omics immune profiling and monitoring at single-cell resolution, enabled by cutting-edge technologies and our highly experienced and knowledgeable physicians, scientists, and technical team.
HIMC is innovation driven and project oriented. We bring the latest technologies for advanced immunology studies and develop the most robust assays and optimized methods on these platforms. Accommodating specific needs of each study and project, our expert team of physicians, scientists, and technicians will provide customizable, integrated services from experimental design, sample processing, data acquisition and processing, to data analysis and management. We apply stringent QC procedures and SOPs to deliver high-quality, accurate, and reproducible results within reasonable time and budget.
Services
Tissue: FFPE (including TMA), frozen tissue sections
- Visium Spatial Gene Expression:
Visium enables comprehensive spatial transcriptomics, capturing gene expression data in intact tissue sections (FFPE/Fixed Frozen and Fresh Frozen), providing valuable insights into tissue architecture and cellular interactions at multi-cellular (55 μm) resolution. - Visium HD Spatial Gene Expression:
Visium HD offers high-definition spatial transcriptomics with enhanced resolution, allowing for more precise localization and detailed analysis of gene expression patterns in complex tissues (FFPE) at single cell (2 μm) resolution. - nCounter System:
The nCounter System provides a robust high sensitivity platform for digital detection and quantification of upto 800 genes RNA, DNA, and protein molecules for gene expression analysis and molecular profiling. - PhenoImager (formerly Vectra® Polaris™)
PhenoImager combines advanced imaging and multiplexed immunofluorescence upto 8 protein markers to deliver detailed spatial phenotyping to visualize and analyze complex tissue architectures and cellular interactions in situ.
Single Cell/Nuclei Suspension: blood, digested/dissociated tissues, cryopreserved or fixed cells
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10x Genomics Single Cell Assays
Single-cell gene expression profiling, paired VDJ sequencing, multiome (ATAC) and surface protein expression on the same cells/nuclei at scale
Single cell in situ
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CosMx High-plex in situ Spatial Molecular Imager:
CosMx provides high-resolution spatial molecular imaging, enabling simultaneous detection, visualization and quantification upto 6000 RNA transcripts and 64 validated protein analytes in FFPE and Fresh Frozen tissue samples at cellular and sub cellular resolution for comprehensive spatial biology studies.
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RNA Scope:
RNA scope detects upto 3 target RNA within intact cells in tissues. Designed to amplify target-specific signals but not background noise from non-specific hybridization.
Supernatent: serum, plasma, tissue lysates, cell culture
- MSD: High-Sensitivity Multiplex Immunoassays
MSD offers advanced multiplex immunoassays capable of detecting and quantifying up to 10 cytokines simultaneously with exceptional sensitivity and specificity. 100 to 1000x times more sensitive than current ELISA assays. Can detect upto 1fg/mL of analytes.
Bioinformatics
From data preprocessing to advanced cell type annotation and pathway analysis, our bioinformatics services can help you analyze your single cell, spatial transcriptomics and bulk RNA data to uncover the intricate details of cellular function and disease mechanisms.
Technologies
HIMC offers the following technology platforms.
Spatial Transcriptomics
Visium
Traditional Visium Spatial Gene Expression is a next-generation molecular profiling solution for mapping transcriptome with morphological context from both FFPE and fresh frozen tissue at 55 μm resolution. It enables detection of ~18,000 human and ~19,500 mouse genes.
- 10 μM tissue sections on charged glass slides.
- Slides are H&E or Immunofluorescence stained and immediately imaged at 4x/10x/20x magnification.
- A 6.5 mm x 6.5 mm or a 11 mm x 11 mm, region of interest
- CytAssist enabled region of interest transferred to spatial slides
- Libraries sequenced at a depth of ~50,000 reads per tissue covered spot
- Based on the tissue type, a 1 to 10 cell resolution is achieved per spot
Visium HD
Visium HD offers high-definition spatial transcriptomics with enhanced resolution, allowing for more precise localization and detailed analysis of gene expression patterns in complex tissues (FFPE) at single cell (2 μm) resolution.Visium HD enables detection of ~18,000 human and ~19,500 mouse genes.
- 10 μM tissue sections on charged glass slides.
- Slides are H&E or Immunofluorescence stained and immediately imaged at 4x/10x/20x magnification.
- A 6.5 mm x 6.5 mm, region of interest
- CytAssist enabled region of interest transferred to spatial slides
- Libraries sequenced at a depth of ~20,000 reads per tissue covered spot
- Single cell resolution is achieved per spot
CosMx™ Spatial Molecular Imager (SMI)
CosMx provides high-resolution spatial molecular imaging, enabling simultaneous detection, visualization and quantification upto 6000 RNA transcripts and 64 validated protein analytes in FFPE and Fresh Frozen tissue samples at cellular and sub cellular (~50 nm) resolution for comprehensive spatial biology studies.
- 10 μM tissue sections are fixed on charged glass slides.
- Uses specific probes/antibodies labeled with a unique barcode system for hybridization or binding.
- Can be customized to add upto 300 additional probes for your genes of interest
- Data analysis performed using AtoMx Spatial Informatics platform. Cloud-based and fully integrated informatics platform for spatial biology.
- Facilitates spatial multomics data analysis and visualization without requiring much coding expertise
RNA Scope
The RNAscope LS Multiplex Fluorescent Assay uses a novel and proprietary method of in situ hybridization (ISH) to simultaneously visualize three RNA targets in formalin-fixed, paraffin embedded (FFPE) tissue or in fresh frozen samples mounted on slides by fluorescent detection.
- Permeabilization: The tissue sections are fixed onto slides and pretreated with RNAscope pretreatment kit to unmask target RNA and permeabilize cells.
- Hybridize: Z probes that are target specific to about 20 base pairs hybridize to target RNA molecules.
- Amplify: Hybridized signal is amplified via sequential hybridization of amplifiers and label probes.
- Visualize: Each dot signal represents a single test target RNA molecule and can be visualized with a microscope.
- Quantification: Single-molecules can be quantified on a cell by cell basis by automated image analysis using HALO software.
PhenoImager
The PhenoImager HT™ (formerly Vectra® Polaris™) is an advanced tissue imager designed to provide unmatched speed, performance, and versatility. It excels in visualizing, analyzing, quantifying, and phenotyping immune cells in situ within Formalin Fixed Paraffin Embedded (FFPE) tissue sections and tissue microarrays (TMAs), significantly advancing disease research.
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Staining
- Tissue sections are mounted on high adhesion slides.
- Slides used for cycles of immunostaining with HIMC-validated primary antibodies, species-specific secondary antibody-HRP polymer, and tyramide signal amplification (TSA) with photostable Opal dyes from Akoya/PerkinElmer.
- Eight cycles are usually performed for a 8-marker panel, plus DAPI counterstaining for nucleus.
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Microscope
- The Akoya/PerkinElmer Vectra automated multispectral microscope takes images across a wide emission spectrum.
- Uses 5 filter cube sets: DAPI, FITC, Cy3, TR, Cy5
- Spectrally unmixed for quantitation of immunofluorescence marker intensity on a pixel-by-pixel basis
- Quantifies and subtracts autofluorescence
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Inform Analysis
- The inForm software also allows advanced image analysis for automated tissue and cell segmentation and phenotyping with machine learning.
- Additional software tools and packages are used for cellular analysis and spatial analysis.
Nanostring nCounter
The NanoString nCounter utilizes multiplex nucleic acid hybridization technology to reliably and reproducibly assess gene expression across up to 800 genes or 228 gene fusions in 12 samples within a single assay. The dual probe design, automated sample processing, and internal controls and normalization algorithms allow for highly reproducible data generated between batches and sites.
- Low sample input, no amplification required
- Rapid Data output
- No coding experience required
10X Genomics (single-cell sequencing)
The 10x Genomics system allows massively parallel, high-throughput single-cell sequencing at reasonable cost per cell/nuclei for ~1,000-50,000 cells per sample, for a variety of applications simultaneously on the same cells:
- General gene expression (mRNA) profiling
- Single Cell Gene Expression (3’)
A versatile solution providing 3' gene expression with options for multiomic analysis that may:- Require full transcript readouts
- Only require gene expression
- Have lower cell input requirements
- Single Cell Gene Expression (3’)
- Single Cell Immune Profiling (5’)
- Comprehensive analysis of immune diversity, combining 5' gene expression with multiomic profiling that may:
- Require full transcript readouts
- Require or may use CRISPR and TCR/BCR sequencing
- Have lower cell input requirements
- Comprehensive analysis of immune diversity, combining 5' gene expression with multiomic profiling that may:
- Paired αβ-TCR sequencing
- Paired heavy and light chain Ig BCR sequencing
- Epitope-specific TCR sequencing using Dextramers
- Surface protein expression using oligo-tagged antibodies (CITEseq) capable of simultaneous detection of >1000 surface markers
- Single cell ATAC for epigenetic regulatory landscape with cellular heterogeneity
- Multiome Sequencing combining single cell gene expression (3’) and ATAC data
MSD: High-sensitivity Multiplex Immunoassays
The MSD system offers advanced multiplex immunoassays with high sensitivity and specificity for simultaneous detection and quantification of up to 10 cytokines. This technology is ideal for comprehensive biomarker studies in both research and clinical settings, utilizing a variety of sample types such as serum, plasma, and tissue lysates. Applications of the MSD system include:
- Cytokine Profiling
- Biomarker Discovery and Validation
- Pharmacokinetics and Pharmacodynamics studies.
Bioinformatics
Interrogate the cellular heterogeneity and gene expression of your sample with our specialised single-cell RNA sequencing analysis services. From data preprocessing to advanced cell type annotation and pathway analysis, we help you uncover the intricate details of cellular function and disease mechanisms.
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Single cell Analysis:
- Alignment and basic gene expression analysis
- Quality control, ambient RNA removal, doublet removal
- Celltype annotation and abundance testing
- Copy number inference and gene enrichment/pathway analysis
- Custom pipeline development
- TCR/BRC analysis
- CRISPR knockout screens
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Spatial Transcriptomics:
Unlock spatial gene expression insights with our cutting-edge spatial transcriptomics analysis services. From data alignment to spatial mapping and differential expression analysis, we help you visualize and understand the complex spatial organization of tissues and cellular interactions.- Alignment and basic gene expression analysis
- Quality control, celltype annotation, deconvolution with single cell data
- Copy number inference and gene pathway enrichment analysis
- Tumour microenvironment analysis
- Pipeline development for data from both Visium HD and CosMx (subcellular resolution)
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Bulk RNA-seq Analysis:
- Alignment to reference transcriptome
- Gene abundance analysis and differential gene expression testing
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