Colorado State University Next Generation Sequencing Core 060915
Transcript of Colorado State University Next Generation Sequencing Core 060915
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Next Generation Sequencing Servicesat Colorado State University
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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
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Laboratory Prep (any questions? Ask Erin.)
Bioinformatics Support (software, databases, training, consulting)
Sequencing Instruments (Illumina, Ion)
Services
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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
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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
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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)
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RNA-Seq
Differential gene expression
Alternative splicing
mRNA (messenger RNA) smRNA (small RNA) miRNA (micro RNA) ncRNA (non-coding RNA)
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EpigeneticsCHiP-Seq, Methyl-Seq, Ribo-Seq
Transcriptional regulation
DNA methylation
Protein-DNA interactions
Translational regulation
Ribosome-mRNA
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Communities & Environment
Community gene expression
Community species IDMetagenomics
Metatranscriptomics
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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
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Host - Parasite
Mixed genotypes:Host genotype(s) &Parasite genotype(s)
Complex cycles +Complex relationships =Complex analysis
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De novo Assembly
Assemble genome or transcriptome without alignment to reference genome
Computationally intensive
Used in numerous bioinformatics pipelines
Francisella tularensis
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Gene Ontology
Biological, physiological, molecular & functional analysis
Integrated with bioinformatics tools
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Pathway Analysis
Biological, biochemical & physiological signaling pathways
Integrated with bioinformatics tools
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Bioinformatics Resources Local pipelines
Cloud-based vendor & opensource pipelines
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Computational Resources
Software
Databases
Cray supercomputer
Clusters
Servers
Staff
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Read Depth Coverage
Integrate lab methods & bioinformatics analysis
Need replicates if feasible
Gierlinski et al., Quantitative Biology, 2015
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DIY sequencing – save $$$
Initial training session
Prepare your own libraries
Run sequencer yourself
For MiSeq & Torrent
$350 / run
Self Service
Ion Torrent
Illumina MiSeq
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Cost Competitive with other Cores
Provide quotes
Includes:Lab prepSequencingBioinformaticsData managementConsulting & TrainingComputational resources
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Contact Us
970-491-8829
web.research.colostate.edu/ngs/(new website coming soon!)