CSU Next Generation Sequencing Core 06/09/2015

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The Next Generation Sequencing Core at Colorado State University provides next generation sequencing and bioinformatics services and support using Illumina and Ion Torrent sequencing platforms for applications such as DNA sequencing, RNA sequencing, epigenetics, metagenomics, and more, drawing on over 10 years of experience and resources including on-campus laboratories, computational infrastructure, and staff expertise. Services include laboratory preparation, sequencing runs, bioinformatics analysis, and training.

Education

Next Generation Sequencing Services
at Colorado State University

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

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 reads
400 bp reads
50 M reads
250 bp reads
100 M reads
200 bp reads
800 M reads
150 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)

Epigenetics
CHiP-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 project
DeCode Project - Icelandic population
Human Longevity Inc. - 100K genomes / yr.
Genome 10K project
i5K – 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 prep
Sequencing
Bioinformatics
Data management
Consulting & Training
Computational resources

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

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This document discusses technologic issues related to genome-wide association studies (GWAS) and follow-up studies. It describes different types of polymorphisms like single nucleotide polymorphisms (SNPs) and copy number variations that can be studied. It discusses strategies for SNP selection and linkage disequilibrium. Different genotyping technologies are also reviewed, along with quality control measures for genotype calls and participant recruitment. Specific results from GWAS of prostate and breast cancer conducted by the Cancer Genetic Markers of Susceptibility (CGEMS) project are summarized.

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This Dissertation explores the particular circumstances of Mirzapur, a region located in the core of India. Mirzapur, with its varied terrains and abundant biodiversity, offers an optimal environment for investigating the changes in vegetation cover dynamics. Our study utilizes advanced technologies such as GIS (Geographic Information Systems) and Remote sensing to analyze the transformations that have taken place over the course of a decade. The complex relationship between human activities and the environment has been the focus of extensive research and worry. As the global community grapples with swift urbanization, population expansion, and economic progress, the effects on natural ecosystems are becoming more evident. A crucial element of this impact is the alteration of vegetation cover, which plays a significant role in maintaining the ecological equilibrium of our planet.Land serves as the foundation for all human activities and provides the necessary materials for these activities. As the most crucial natural resource, its utilization by humans results in different 'Land uses,' which are determined by both human activities and the physical characteristics of the land. The utilization of land is impacted by human needs and environmental factors. In countries like India, rapid population growth and the emphasis on extensive resource exploitation can lead to significant land degradation, adversely affecting the region's land cover. Therefore, human intervention has significantly influenced land use patterns over many centuries, evolving its structure over time and space. In the present era, these changes have accelerated due to factors such as agriculture and urbanization. Information regarding land use and cover is essential for various planning and management tasks related to the Earth's surface, providing crucial environmental data for scientific, resource management, policy purposes, and diverse human activities. Accurate understanding of land use and cover is imperative for the development planning of any area. Consequently, a wide range of professionals, including earth system scientists, land and water managers, and urban planners, are interested in obtaining data on land use and cover changes, conversion trends, and other related patterns. The spatial dimensions of land use and cover support policymakers and scientists in making well-informed decisions, as alterations in these patterns indicate shifts in economic and social conditions. Monitoring such changes with the help of Advanced technologies like Remote Sensing and Geographic Information Systems is crucial for coordinated efforts across different administrative levels. Advanced technologies like Remote Sensing and Geographic Information Systems 9 Changes in vegetation cover refer to variations in the distribution, composition, and overall structure of plant communities across different temporal and spatial scales. These changes can occur natural.

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CSU Next Generation Sequencing Core 06/09/2015

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!)

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