Burt, Dave - The Roslin Institute - University of Edinburgh

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RNA-Seq BioinformaticsFastqcfastxSoap2Our owndatabaseCounts <strong>of</strong> RNA-Seqtags for each geneedgeR50
Differential Gene ExpressionGene Symbol Gene Description adjPVal FCART1 ADP-ribosyltransferase 1 [Gallus gallus] 2.13E-235 166IL28B Interferon lambda, Interleukin 28 ; [Gallus gallus] 5.60E-09 159PTX3 pentraxin-related gene, rapidly induced by IL-1 beta [Gallus gallus] 1.63E-17 89IFNB1 Interferon type B Precursor [Gallus gallus] 4.69E-07 71VEPH1 ventricular zone expressed PH domain homolog 1 (zebrafish) [Gallus gallus] 2.70E-17 57MX2 myxovirus (influenza virus) resistance 2 (mouse) [Gallus gallus] 1.21E-66 52RSAD2 radical S-adenosyl methionine domain containing 2 [Gallus gallus] 5.22E-61 48IFIT5 interferon-induced protein with tetratricopeptide repeats 5 [Gallus gallus] 4.62E-15 42TMPRSS2 transmembrane protease, serine 2 [Gallus gallus] 9.01E-26 42LYG1 lysozyme G-like 1 [Gallus gallus] 2.58E-48 41LOC768689 hypothetical protein LOC768689 [Gallus gallus] 1.72E-10 -15TNFRSF13C tumor necrosis factor receptor superfamily, member 13C [Gallus gallus] 1.18E-10 -15DAAM1L dishevelled-associated activator <strong>of</strong> morphogenesis 1-like [Gallus gallus] 2.89E-13 -16LOC424146 hypothetical LOC424146 [Gallus gallus] 6.77E-20 -16FAM5B family with sequence similarity 5, member B [Gallus gallus] 2.32E-45 -17PTPN5 protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched) [Gallus gallus] 3.45E-38 -17DCLK1 doublecortin-like kinase 1 [Gallus gallus] 1.05E-15 -23PROKR2 Prokineticin receptor 2 [Gallus gallus] 2.55E-18 -37AMY1C amylase, alpha 1C (salivary) [Gallus gallus] 9.82E-09 -40CLRN3 clarin 3 [Gallus gallus] 3.60E-106 -4951
Page 1 and 2: Next Generation SequencingCurrent S
Page 3 and 4: First Generation SequencingFrederic
Page 5 and 6: Genetic Maps• Genetic markers (e.
Page 7 and 8: QTL Mapping• QTL not mapped preci
Page 9 and 10: Genomic Tools• Expressed sequence
Page 11 and 12: Genomic Tools• Expressed sequence
Page 13 and 14: Sequencing TechnologiesNGS technolo
Page 15 and 16: Clonal Single Molecule ArraysAttach
Page 17 and 18: Base Calling from Raw DataT G C T A
Page 19 and 20: Applications19
Page 21 and 22: Avian GenomesFlightSmall genomeUniq
Page 23 and 24: Computational Pipeline forEnsembl/C
Page 25 and 26: Changes in gene family size along e
Page 27 and 28: Compare Rates of EvolutionSelection
Page 29 and 30: Rates Mammals > Birdsmovement of B
Page 31 and 32: Applications31
Page 33 and 34: Genome Wide Selection• Genotype 1
Page 35 and 36: % of SNPsNumber of SNPs/cMNumber of
Page 37 and 38: Annotation of SNPs%5045403530252015
Page 39 and 40: Final Panel Selection• 600K panel
Page 41 and 42: Applications of SNP Panel• Genomi
Page 43 and 44: AcknowledgementsFundingBBSRC/Defra
Page 45 and 46: RNA-Seq45
Page 47 and 48: Gene Models: TEF47
Page 49: Experimental Design• 3 spleen sam
Page 53 and 54: Enrichment Analysis: MicroarrayMicr
Page 55 and 56: Advantages of RNA-Seq55
Page 57 and 58: AcknowledgementsFundingBiotechnolog
Page 59: Applications59
Page 62 and 63: MeDIP-Seq: NPAS462
Page 64 and 65: Sequencing TechnologiesNGS technolo
Page 66: Sequencing TechnologiesNGS technolo

Burt, Dave - The Roslin Institute - University of Edinburgh

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