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Services

The Genomics Core facility maintains a significant portfolio of instrumentation and expertise to support a broad spectrum of genomic services such as various types of quality control, advanced sample and library preparation for single-cell/nucleus and for bulk, high-throughput sequencing, real-time PCR and digital PCR analysis.

The key platforms for sequencing involve NextSeq2000 and MiSeq sequencers (Illumina). These platforms offer a large variety of sequencing configurations ranging from 1 x 50 bp single end (SE) to 2 x 300 bp paired end (PE) or 1 x 600 bp single end (SE) sequencing, generating up to 1.8 billion read pairs per sequencing run.

The VCU Genomics Core works closely with other VCU facilities, to allow for streamlined support for tissue sectioning and staining (Tissue and Data Acquisition and Analysis), data analysis (Bioinformatics Shared Resource) and data storage (VCU High Performance Research Computing Core).

Examples of common services:

Sample preparation and quality control

  • DNA and/or RNA extraction
  • DNA fragmentation
  • concentration assessment
  • RNA integrity numbers
  • fragment length distribution
  • size selection/purification
  • sample pooling

Transcriptome sequencing

  • transcriptome sequencing based on poly-A enrichment (RNA-seq)
  • total RNA sequencing with ribosomal depletion (RNA-seq)
  • small RNA sequencing (microRNA-seq)
  • circular RNA sequencing (circRNA-seq)

Single-cell/nucleus sequencing

  • single cell/nucleus RNA sequencing (sc/nRNA-seq)
  • single cell/nucleus ATAC sequencing (sc/nATAC-seq)
  • single cell/nucleus multiomic sequencing (sc/n-seq)
  • spatial transcriptomics

Microbiome sequencing

  • 16 S rRNA taxonomic profiling
  • metagenome sequencing
  • meta-transcriptome sequencing

Epigenome sequencing

  • methyl-binding domain sequencing (MBD-seq)
  • chromatin immunoprecipitation sequencing (ChIP-seq)
  • assay for transposase-accessible chromatin sequencing (ATAC-seq)
  • whole genome bisulfite sequencing (WGBS)

DNA sequencing

  • de novo sequencing
  • whole genome sequencing (WGS)
  • whole exome sequencing (WES)
  • amplicon sequencing

Quantitative PCR assays

  • C. bovis detection
  • Custom qPCR or dPCR assays