colorado state university next generation sequencing core 060915

Next Generation Sequencing Servicesat Colorado State University

Next Generation Sequencing Core (NGS) Colorado State University

Vice President for Research OfficeInfectious Disease Research Center

NGS Core

10 years in operationCSUFoothills Campus

(south side)

Research Innovation Center

Laboratory Prep (any questions? Ask Erin.)

Bioinformatics Support (software, databases, training, consulting)

Sequencing Instruments (Illumina, Ion)

Services

Ion Proton Ion TorrentIllumina MiSeqIllumina NextSeq

Instruments

10 M reads400 bp reads

50 M reads250 bp reads

100 M reads200 bp reads

800 M reads150 bp reads

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

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)

RNA-Seq

Differential gene expression

Alternative splicing

mRNA (messenger RNA) smRNA (small RNA) miRNA (micro RNA) ncRNA (non-coding RNA)

EpigeneticsCHiP-Seq, Methyl-Seq, Ribo-Seq

Transcriptional regulation

DNA methylation

Protein-DNA interactions

Translational regulation

Ribosome-mRNA

Communities & Environment

Community gene expression

Community species IDMetagenomics

Metatranscriptomics

Population Scale SequencingPopulation genetics

Phylogenetics

Genetic drift

Pedigrees

1,000 Genomes projectDeCode Project - Icelandic populationHuman Longevity Inc. - 100K genomes / yr.Genome 10K projecti5K – 5K insect genomes

Host - Parasite

Mixed genotypes:Host genotype(s) &Parasite genotype(s)

Complex cycles +Complex relationships =Complex analysis

De novo Assembly

Assemble genome or transcriptome without alignment to reference genome

Computationally intensive

Used in numerous bioinformatics pipelines

Francisella tularensis

Gene Ontology

Biological, physiological, molecular & functional analysis

Integrated with bioinformatics tools

Pathway Analysis

Biological, biochemical & physiological signaling pathways

Integrated with bioinformatics tools

Bioinformatics Resources Local pipelines

Cloud-based vendor & opensource pipelines

Computational Resources

Software

Databases

Cray supercomputer

Clusters

Servers

Staff

Read Depth Coverage

Integrate lab methods & bioinformatics analysis

Need replicates if feasible

Gierlinski et al., Quantitative Biology, 2015

DIY sequencing – save $$$

Initial training session

Prepare your own libraries

Run sequencer yourself

For MiSeq & Torrent

$350 / run

Self Service

Ion Torrent

Illumina MiSeq

Cost Competitive with other Cores

Provide quotes

Includes:Lab prepSequencingBioinformaticsData managementConsulting & TrainingComputational resources

Contact Us

970-491-8829

ngscore@colostate.edu

web.research.colostate.edu/ngs/(new website coming soon!)