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)
  • Small RNA sequencing (miRNA-Seq)
  • Whole exome sequencing
  • Targeted resequencing
  • Whole genome sequencing
  • Chromatin immunoprecipitation sequencing (ChIP-Seq)
  • Methylation sequencing (Methyl-Seq)
  • Copy number variation sequencing (CNV-Seq)
  • ATACseq

10X Single Cell Sequencing

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.

  • Chromium™ Single Cell 3’ Library Construction
  • Chromium™ Single Cell 5’ Immune Library Construction (Single Cell V(D)J + 5’ Gene Expression)
  • Chromium™ Single Cell ATAC Solution
  • Chromium Single Cell Multiome ATAC + 3’ Gene Expression

Spatial Transcriptomics

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.

Two spatial transcriptomics technologies are commercially available today: (1) The 10X Visium spatial transcriptomics from 10X Genomics and (2) GeoMx digital spatial profiler (GeoMx DSP) from Nanostring Technologies. 10X Visium technology can profile whole transcriptome from fresh or FFPE tissues. GeoMx DSP can profile both RNA & Protein for whole transcriptome or targeted panels including:

  • The GeoMx® Cancer Transcriptome Atlas (CTA) (1833 genes)
  • GeoMx Human Whole Transcriptome Assay (WTA) (>20000 genes)
  • GeoMx Mouse Whole Transcriptome Assay (>21000 genes)
  • GeoMx Immune Pathways Panel (96 genes)

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 customized data analysis
  • Online data delivery, long term storage and data retrieval
  • Data analysis tutorial

Other Services

Educational workshops are offered annually. Our core facility also provides RNA/DNA extraction; RNA/DNA quality control and quantification; cDNA synthesis for quantitative-PCR; and QRT-PCR.