EpiChrom 2019 - Updates in Epigenomics at the NGI
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Slides from my talk at the SciLifeLab EpiChrom 2019 meeting: https://www.scilifelab.se/epichrom-2019/ # New epigenomics services at the National Genomics Infrastructure A quick walkthrough of new library preparation methods on offer to study epigenetic signals at the National Genomics Infrastructure.
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EpiChrom 2019 - Updates in Epigenomics at the NGI
- 1. Phil Ewels NGI Applications Development Facility phil.ewels@scilifelab.se New epigenomics services
- 4. Guidelines and support Available to all Swedish researchers State-of-the-art infrastructure All icons © flaticon.com
- 5. Meetings QC & Library Preparation Sequencing Genotyping Data analysis & delivery All icons © flaticon.com
- 7. 2018 61,471samples 975projects 588.6 x1012 base pairs 1X Human genome every minute
- 12. Illumina NovaSeq 6000 Illumina HiSeq One HiSeq X lane ~ one 30x coverage Human genome 120 Gbp One NovaSeq lane ~ six 30x coverage Human genomes 750 Gbp
- 13. Illumina NovaSeq 6000 Illumina HiSeq One HiSeq 2500 lane ~ 12 RNA samples with 20M reads 250 M reads One NovaSeq lane ~ 120 RNA samples with 20 M reads 2500 M reads
- 14. Production methods Validated library-preps run routinely Under development Testing new kits, actively looking for collaborators Scaling up Method is robust, now gaining experience and automation Planned Planning for the future, not yet tested
- 15. Epigenetics Methods Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq poly-A capture rRNA removal Low input Degraded
- 16. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq PacBio isoform Nanopore isoform Single cell RNA 10x Genomics Chromium See also: Eukaryotic Single Cell Genomics (ESCG) http://escg.se/ Epigenetics Methods
- 17. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq PCR-free Low input Ideal for ChIP-seq! Epigenetics Methods
- 18. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq WGBS Whole genome bisulfite seq RRBS Reduced representation bisulfite seq Arrays Infinium MethylationEPIC Epigenetics Methods
- 19. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq oxBS Oxidative bisulfite seq for hydroxymethylation Single cell bisulfite Low input Epigenetics Methods
- 20. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq Wikimedia Commons - ZaZo0o Epigenetics Methods
- 21. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq Epigenetics Methods -1 10 Sample 1 -1 10 -1 10 Sample 3Sample 2 Enrichment over promoter regions, +/-1 kbp High Low NGI pilot project
- 22. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq Epigenetics Methods Differentially Expressed Genes: RNA vs ATACseq NGI pilot project
- 23. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq Single cell ATAC-seq 10x Genomics Chromium ATAC-seq Epigenetics Methods
- 24. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq Crosslink DNA Cut with RE End fill with biotin Ligate Shear Sequence Pull down Lieberman-Aiden et. al. Science (2009) Epigenetics Methods
- 25. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq High Low Ulianov et. al. International review of cell and molecular biology (2015) Epigenetics Methods
- 26. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq High Low Rao et. al. Cell (2014) Epigenetics Methods
- 30. Hi-C Modifications Methylation Enrichment DNA-seq RNA-seq ATAC-seq PacBio enrichment CRISPR amplification-free Epigenetics Methods ChIP-seq
- 32. support@ngisweden.se NGI Stockholm Applications Development Facility phil.ewels@scilifelab.se Phil Ewels We want to hear from you! https://ngisweden.scilifelab.se