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HTS Platforms

HTS Platforms. Illumina SOLiD Roche/454 Complete Genomics Helicos Pacific Biosciences IonTorrent * Oxford Nanopore. PCR Amplification & Sequence by synthesis/ligation/ hyb. Single molecule - no Amp. Sequence by synthesis. Nanopore. Illumina Paired-End Sequencing. Ion Torrent.

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HTS Platforms

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  1. HTS Platforms • Illumina • SOLiD • Roche/454 • Complete Genomics • Helicos • Pacific Biosciences • IonTorrent* • Oxford Nanopore PCR Amplification & Sequence by synthesis/ligation/hyb Single molecule - no Amp. Sequence by synthesis Nanopore

  2. IlluminaPaired-End Sequencing

  3. Ion Torrent

  4. Oxford Nanopore

  5. Single Cell Genomics • Goal: analyze cell-to-cell differences in transcriptome, epigenetic signatures • Learn about: • Spread of cancer cells • Differentiating stem cells into specialized cells (e.g., neurons, cardiomyocytes) • RNAs localized to specific cellular regions (e.g., dendrites) • Difficulties • Small sample size (i.e., low RNA/DNA content) • Cell sorting

  6. Single Cell Genomics • Advances in: • Microfluidics • Separating single cells • Enzymatic digestion • Laser-capture microdissection • Cell lysis • Whole genome/transcriptome amplification

  7. Variants on RNA-seq • GRO-seq • Ribosomal Footprinting

  8. Ribosomal Footprinting • Measure translation • Assess ribosomal pausing Ingolia et al. 2009

  9. GRO-seq • Global Run-On Sequencing - maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide Core et al. 2008, Lis Lab

  10. GRO-seq Core et al. 2008, Lis Lab

  11. GRO-seq Core et al. 2008, Lis Lab

  12. Thomas Sharpton

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