Pathology

Services

Services

* Please note that sequencing will be separate for Visium, GeoMx, and StereoSeq

Long Read Sequencing (Third Generation) and Next Generation Sequencing (Second Generation)

DNA and RNA sequencing is the process of determining the nucleotide order of a given DNA fragment. The nucleotide sequence encodes the necessary information that allows living things to survive and reproduce. Determining the sequence is therefore useful in researching into how organisms live. Our core facility provides many sequencing options to meet your individual needs, utilizing (a) Oxford NanoPore GridIONx5 Long-Read Sequencing (by reading the nucleotide sequences at the single molecule level), and (b) Illumina Short-Read Sequencing (by massive parallel sequencing of millions of DNA fragments and yielding substantially more throughput reads quickly).

  • Whole Transcriptome Sequencing (RNA-Seq)
  • Copy Number Variation Sequencing (CNV-Seq)
  • Small RNA Sequencing (miRNA-Seq)
  • Chromatin Immunoprecipitation Sequencing (Chip-Seq)
  • Methylation Sequencing (Methyl-Seq)

Single Cell Multiomics

10X Single Cell Library Construction

The Chromium 10x Genomics 3’ Single Cell Gene Expression Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells. The Chromium Single Cell Immune Profiling simultaneously examines the cellular context of the adaptive immune response and immune repertoires of hundreds to tens of thousands of T and B cells in human or mouse tissue on a cell-by-cell basis. The newest one is the Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin), which accelerates the understanding of the regulatory landscape of the genome, providing insights into cell variability.

  • 3’ GEX Library Prep (Fresh Cell)
  • 3’ GEX Fixed/FFPE RNA Profiling (FRP) Library Prep
  • 3’ GEX + FB (Single Cell Hashing) Library Prep
  • TCR Library Prep
  • 5’ GEX + TCR Library Prep
  • 5’ GEX + TCR + BCR Library Prep
  • 5’ GEX + FB (Single Cell Hashing) Library Prep
  • ATAC Library Prep 
  • Multiome (ATAC + 3’GEX) Library Prep

BD Rhapsody

The BD Rhapsody™ Single-Cell Analysis System offers a fast and easy way to collect a wealth of information about individual cells, including their genes and proteins. This is achieved through a unique cartridge system and a sophisticated barcoding technique. The collected data can then be used to create specialized libraries for next-generation sequencing (NGS), a powerful tool for analysing massive amounts of genetic information. By analysing these NGS libraries, researchers gain a deep understanding of individual cells, uncovering hidden patterns and insights invisible to traditional methods.

  • BD Rhapsody™ WTA Library Prep
  • BD Rhapsody™ WTA + Sample Tag Library Prep
  • BD Rhapsody™ WTA + Sample Tag + AbSeq Library Prep

Spatial Genomics

Each organ of a complex organism consists of diverse cell types that often interact in highly structured manners under distinct microenvironments. Such highly structured spatial heterogeneity enables the organism to function correctly and efficiently. To fully understand gene functions in a given cell type, one must study gene expression in the context of the location of the cells in the tissue. Spatial transcriptomics is a recently developed transformative technology that combines the strengths of the global transcriptional analysis of bulk RNASeq and In-situ hybridization, providing transcriptomics data in the context of spatial locations of the cells in situ.

Six spatial transcriptomics technologies are commercially available today: (1) The 10X Visium spatial transcriptomics from 10X Genomics (2) Visium HD spatial gene expression from 10X Genomics (3) GeoMx digital spatial profiler (GeoMx DSP) from NanoString Technologies (4) CosMx SMI for single-cell imaging from NanoString Technologies (5) Xenium single cell spatial imaging platform from 10X Genomics and (6) Stereo-seq Transcriptomics Solution from STOmics. Fresh or FFPE tissues can be applied to 10X Visium, GeoMx DSP, and CosMx and fresh or PFA fixed tissues to Stereo-seq:

10X Visium 

  • Visium Gene Expression (GEX)
  • Visium Tissue Optimization (TO)
  • Visium Whole Transcription Analysis (WTA) with CytAssist
  • Visium Whole Transcription Analysis + Protein Expression (WTA + PEX)

Visium HD

  • Human or Mouse Whole Transcription Analysis (WTA)

GeoMx DSP 

  • GeoMx Whole Transcriptome Analysis for Human & Mouse
  • GeoMx Cancer Transcriptome Analysis for Human
  • GeoMx Protein Profiling

CosMx SMI

  • CosMx Universal RNA Panel for Human
  • CosMx Immuno-oncology RNA Panel for Human
  • CosMx Neuro RNA Panel for Mouse

Xenium 

  • 10X Xenium Panel (users provide specific gene panel)

StereoSeq

  • Whole Transcriptome Analysis for Any Species

Advanced Data Analysis

The TCGB has various academic and commercial data mining software and other resources for genomic data analysis, including Partek flow, VarSeq, Ingenuity Pathway Analysis, Falcon automated genomic analysis system, Hoffman2 data analysis clusters, Illumina basespace Sequencing Hub professional, Amazon cloud HIPAA compliant research computing, and storage system server.

  • Standard NGS Analysis
  • Advanced and customised data analysis, including 10X single cell and spatial data analysis
  • Online data delivery, long term storage and data retrieval
  • Data analysis tutorial
  • BioTuring

Other Services

The TCGB hosts not only informative seminars on cutting-edge technologies every one to two months but also annual educational workshops offering comprehensive learning experiences. Our core facility also provides:

  • RNA/DNA extraction
  • RNA/DNA quality control and quantification
  • RNA/DNA Purification
  • cDNA synthesis for quantitative-PCR
  • QRT-PCR
  • qPCR Library Quantification
  • Covaris Fragmentation
  • Size-selection
  • Vacuum Concentration