A brief overview of the Next Generation Sequencing Core at Colorado State University.

1. Next Generation Sequencing Services
at Colorado State University

2. Next Generation Sequencing Core (NGS)
Colorado State University
Vice President for Research Office
Infectious Disease Research Center
NGS Core
10 years in operation
CSUFoothills Campus
(south side)
Research Innovation Center

3. Laboratory Prep
(any questions? Ask Erin.)
Bioinformatics Support
(software, databases, training, consulting)
Sequencing Instruments
(Illumina, Ion)
Services

4. Ion Proton Ion TorrentIllumina MiSeqIllumina NextSeq
Instruments
10 M reads
400 bp reads
50 M reads
250 bp reads
100 M reads
200 bp reads
800 M reads
150 bp reads

5. NextGen Seq Research
DNA-Seq
(replication)
RNA-Seq
(transcription)
RNA-Seq
(microRNA)
Ribo-Seq
(translation)
Populations
Host-Parasite
Metagenomics
Methyl-Seq CHiP-Seq
Epigenetics
Organismal Environmental
Metatranscriptomics

6. DNA-Seq
Whole genome sequencing
Targeted resequencing
(genes, exons, exomes, promoters, enhancers, etc.)
SNP’s, MNP’s
(single & multiple nucleotide polymorphisms)
INDEL’s
(insertions, deletions)
Structural rearrangements
(duplications, inversions, translocations, copy number variation)

7. RNA-Seq
Differential gene expression
Alternative splicing
mRNA (messenger RNA)
smRNA (small RNA)
miRNA (micro RNA)
ncRNA (non-coding RNA)

8. Epigenetics
CHiP-Seq, Methyl-Seq, Ribo-Seq
Transcriptional regulation
DNA methylation
Protein-DNA interactions
Translational regulation
Ribosome-mRNA

9. Communities & Environment
Community gene expression
Community species IDMetagenomics
Metatranscriptomics

10. Population Scale Sequencing
Population genetics
Phylogenetics
Genetic drift
Pedigrees
1,000 Genomes project
DeCode Project - Icelandic population
Human Longevity Inc. - 100K genomes / yr.
Genome 10K project
i5K – 5K insect genomes

11. Host - Parasite
Mixed genotypes:
Host genotype(s) &
Parasite genotype(s)
Complex cycles +
Complex relationships =
Complex analysis

12. De novo Assembly
Assemble genome or transcriptome without alignment to reference genome
Computationally intensive
Used in numerous bioinformatics pipelines
Francisella tularensis

13. Gene Ontology
Biological, physiological, molecular & functional analysis
Integrated with bioinformatics tools

14. Pathway Analysis
Biological, biochemical & physiological signaling pathways
Integrated with bioinformatics tools

15. Bioinformatics Resources
Local pipelines
Cloud-based vendor & opensource pipelines

16. Computational Resources
Software
Databases
Cray supercomputer
Clusters
Servers
Staff

17. Read Depth Coverage
Integrate lab methods & bioinformatics analysis
Need replicates if feasible
Gierlinski et al., Quantitative Biology,
2015

18. DIY sequencing – save $$$
Initial training session
Prepare your own libraries
Run sequencer yourself
For MiSeq & Torrent
$350 / run
Self Service
Ion Torrent
Illumina MiSeq

19. Cost
Competitive with other Cores
Provide quotes
Includes:
Lab prep
Sequencing
Bioinformatics
Data management
Consulting & Training
Computational resources

20. Contact Us
970-491-8829
ngscore@colostate.edu
web.research.colostate.edu/ngs/
(new website coming soon!)