Next Generation Sequencing
NGS Platforms
NEW INSTRUMENT
Illumina NovaSeq X Plus:
Key features of the NovaSeq X include scalability, increased run speed, and substantially higher throughput. With 1.5B, 10B, and 25B cluster flow cells available, the platform offers flexibility to meet a wide range of project needs and improves turnaround times by reducing delays associated with filling large flow cells. The NovaSeq X Plus is currently the highest-throughput next-generation DNA sequencing platform available, capable of generating up to 16 Tb of data, or approximately 104 billion paired-end reads, in a single run. NovaSeq X Specifications
Illumina NextSeq 2000:
This system brings GSF 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 2000 can generate up to 1.8 Billion sequencing reads (Single Reads) on a P4 flow cell. NextSeq Specifications.
Illumina MiSeq i100: This system is focused on applications such as targeted sequencing, 16S metagenomics, small genome sequencing, targeted gene expression profiling and other amplicon sequencing. Miseqi100 can generate up to 25 million sequencing reads (Single Reads) on a flow cell and sequence 2 x 500 bp read lengths. MiSeq Specifications.
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
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
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
16S amplicon sequencing
Whole Genome Metagenomic sequencing
Metatranscriptomic analysis
DNA/chromatin fragmentation by Covaris
DNA / RNA quality analysis: TapeStation assay, Qubit (Picogreen) assays
qPCR services
To submit a sample, please complete the appropriate forms and send them to our NGS representative at flsi-illuminaseq-g@vt.edu.
mRNA- and small RNA-Seq Submission Forms:
VT Researcher-Project and RNA Submission Form for RNA-QC
VT Researcher-Project and RNA Submission Form for RNA-Seq
DNA-Seq Sample Submission Forms
VT Researcher-Project and DNA Submission Form for DNA-Seq
Metagenomic Sample Submission Forms:
VT Researcher-16S Sample Submission Form
Illumina lists a range of specifications and GSF 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.
RNA and DNA QC
Includes NanoDrop, Qubit, or TapeStation
2 days to 1 week
GSF 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. Please contact the GSF for current turnaround time estimates.
Sequencing
Please contact the GSF for current turnaround time estimates.
Due to limitations in our storage capacity, the GSF can only maintain customer data for a period of 90 days following completion of work. Any data files older than 90 days are subject to removal from our systems in order to make room for new sequencing runs. We strongly encourage our users to download and check the integrity of their sequencing data files (e.g. md5sums) as soon as possible, and to utilize appropriate long-term storage and curation resources for their research data. Please visit here for more information on current Virginia Tech guidelines and best practices with regards to Data Management.