csu next generation sequencing core 06/09/2015
TRANSCRIPT
Next Generation Sequencing Servicesat Colorado State University
Next Generation Sequencing Core (NGS)
Colorado State UniversityVice President for Research Office
Infectious Disease Research CenterNGS 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 Sequencing
Population 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
