Immunogenomics

Head: Shanshan HOWLAND, Ph.D.
Email:  Shanshan_Howland@a-star.edu.sg

The Immunogenomics Platform facilitates transcriptome analysis of bulk and single cell samples, immune repertoire sequencing, targeted sequencing, viral/microbial sequencing as well as the latest multi-omics technologies.

Overview

The SIgN Immunogenomics Platform supports all aspects of transcriptomics, epigenomics and multi-omics research with high-level technical expertise and openness to embracing new technologies. We provide research consultations and engage with scientists to ensure that they reach their experimental goals and stay on budget using the most suitable technology platforms. Our experienced staff apply stringent quality control measures throughout the workflows to ensure accurate, reliable and reproducible results. A*STAR scientists are welcome to approach us to co-develop custom applications that require a Next Generation Sequencing (NGS) readout.

Approach

We develop in-house methods and implement commercial solutions to transform biological samples (tissues, cells, purified nucleic acids, or slides) into high-quality libraries ready for NGS. We devise the best possible approach depending on sample number, input, quality, fresh or fixed, cost, and turnaround time, linking up with NGS providers to sequence your samples separately or in pooled lanes with our other projects.

Together with the SIgN Computational Immunology Platform, we deliver an end-to-end solution to tackle immunological questions. We also work downstream of other SIgN platforms such as Flow Cytometry and Single-Cell Cloning Platform (Beacon Optofluidic System) to sequence cells isolated by these technologies.

Equipment

Figure 1: Equipment available in the SIgN Immunogenomics laboratory

Application and Technologies

• Bulk RNA sequencing, including RNA extraction and QC, specializing in low input samples
• Single cell/nuclei RNA sequencing and multi-omics
  • Droplet-based platforms — 10x Genomics & MGI
  • Microwell array (good for fragile cells and granulocytes) — BD Rhapsody
  • Combinatorial indexing (scale up exponentially for cheap) — Parse Biosciences & Scale Biosciences
  • One cell per well (for truly rare cells) — Smart-seq2
  • Support for fixed samples (infectious samples, collecting samples over time) — 10x Genomics Flex, Parse, Scale
  • Support for protein readout via oligo-barcoded antibodies
  • Support for sample multiplexing (e.g. “cell hashing”) to reduce costs
• Single cell immune repertoire sequencing (TCR/BCR or V(D)J sequencing) with multi-platform support
• Epigenomic studies (methylation, single cell ATAC-seq)
• Pathogen and microbiome genome sequencing
• Spatial transcriptomics — GeoMx Digital Spatial Profiler allows quantification of whole transcriptome and optionally 570+ proteins from spatially-selected regions on FFPE slides