Next Generation Sequencing Services

GSC scientist using the NovaSeq 6000 instrument.

Platforms | Services | Sample Submission | Deliverables | Turnover Times | Pricing

Overview

The following NGS technologies and services are offered:

NGS Platforms

  • Illumina NovaSeq 6000: This is Illumina’s groundbreaking platform, which enables scalable throughput and flexibility for any sequencing method, genome, and scale of project. GSC can leverage this instrument using 1, 2, 3, and 4 lane flow cells, to multiplex 96-384 samples or more per run, thus providing the best cost-to-benefit NGS services to VT researchers. NovaSeq can generate 8-10 billion sequencing reads (Single Reads) on a S4 flow cell and sequence 2 x 150 bp read lengths. NovaSeq Specifications.
  • Illumina NextSeq 500: This system brings GSC the flexibility for a fast turnaround for smaller projects. With tunable output and high data quality, it provides flexibility for whole-genome, transcriptome, and targeted resequencing. NextSeq can generate up to 400 million sequencing reads (Single Reads) on a High Output flow cell and sequence 2 x 150 bp read lengths. NextSeq Specifications.
  • Illumina MiSeq: This system is focused on applications such as targeted sequencing, 16S metagenomics, small genome sequencing, targeted gene expression profiling and other amplicon sequencing. Miseq can generate up to 25 million sequencing reads (Single Reads) on a High Output flow cell and sequence 2 x 300 bp read lengths. MiSeq Specifications.
  • Thermo Ion S5: The Ion S5™ next-generation sequencing system enables simple targeted sequencing workflows at an affordable price, without compromising on performance or reliability. Ion S5 Specifications.

Services

Transcriptomics

  • mRNA-Seq: Stranded and non-stranded, high levels of multiplexing up to 96 or more samples on NovaSeq
    • Standard amounts, Stranded-Seq: 500 ng total RNA, RIN =>8
    • Low Input amounts, Stranded-Seq: 5 ng – 100 ng total RNA
    • Ultra Low Input amounts, Non-Stranded-Seq: 1-1000 cells or 10 pg - 10 ng
  • Total RNA-Seq - Stranded: 5-250 ng
  • Small RNA-Seq: 1 ug, multiplexing up to 48 samples/NextSeq run
  • Partially degraded samples - Stranded and Non-Stranded: LCM, FFPE samples, both stranded and non-stranded, 50 -100 ng
  • Microbial rRNA depletion and RNA-Seq with amounts as low as 1-5 ug of total RNA

Genomics

  • Whole Genome Sequencing
    • Human / Animal / Plant
    • Microbial
    • As low as 1 ng
  • De novo Sequencing
  • Exome/Targeted capture re-sequencing: Enables high sequencing depths
    • Agilent and Illumina platforms
    • Human, Mouse, Canine and other species
  • Targeted re-sequencing: High levels of multiplexing up to 200 samples / MiSeq run
    • PCR Amplicon sequencing
    • Illumina and Agilent platforms

Gene Regulation

  • ChIP-Seq
    • Transcription factor analysis
    • Histone modifications
  • DNA Methylation
    • MeDIP- and MBD-Seq
    • MethylC-Seq
    • Agilent SureSelect MethylC-Seq
    • Nucleosome Mapping
      • FAIRE-Seq and DNAse I-Seq

Metagenomics

  • 16S / 18S / ITS amplicon sequencing
  • Whole Genome Metagenomic sequencing
  • Metatranscriptomic analysis

Other Services

  • DNA/chromatin fragmentation by Covaris
  • DNA / RNA quality analysis: BioAnalyzer / TapeStation assay, Qubit (Picogreen) assays
  • qPCR services

Sample Submission

To submit a sample, please complete the appropriate forms and send them to our NGS representative at flsi-illuminaseq-g@vt.edu.

Deliverables

Illumina lists a range of specifications and GSC tries its best to deliver within these specifications. The deliverables also depend on the type (RNA, DNA, low diversity samples etc.) and quality of samples submitted (sub optimal amounts, sample degradation, contamination, whether recommended protocols were used for sample extraction, whether libraries were customer generated etc.). These issues will be discussed before, during and after completion of the project.

Turnover Times


RNA and DNA QC

  • Includes NanoDrop, Qubit, BioAnalyzer, or TapeStation
  • 2 days to 1 week
  • GSC will send the QC data, and discuss whether the samples can move forward for library preps and sequencing

Library Preparation

  • Includes library preps, QC and quantitation
  • 1-3 weeks depending on sample quality, sample number, type of library prep, and previous samples in the queue.
  • The clock is reset if the library preps fail and the user submits replacement samples

Sequencing

  • NextSeq: Sequencing times of 1-2 days depending on the length of sequencing. There is no lane sharing in NextSeq.
  • NovaSeq: Sequencing times of 1-2 days depending on the length of sequencing.
  • MiSeq: 1-3 days depending on the length of sequencing.

Pricing

For up-to-date information on the pricing structure of GSC services, as well as official refund and delivery policies, please reference our downloadable pricing guide.