Virtual tour of a Genomics lab

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Virtual tour of a Genomics lab

• Dr Neil Graham
• Plant Sciences Division
• http//plantsci.nottingham.ac.uk/staff/graham/

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Automated equipment in a genomics lab

• What you need / consider to process a large
  genomic / EST library
• Sample Preparation
• Size of sample plate
• Colony picking
• DNA extraction
• PCR / sequencing reaction
• Analysis
• Sequencing
• Arraying
• SNP

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Equipment in a genomics lab

• What you need to process a large genomic / EST
  library
• Sample Preparation
• Size of sample plate
• Colony picking
• DNA extraction
• PCR / sequencing reaction
• Analysis
• Sequencing
• Arraying
• SNP

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Size of sample plate

• Dependant on number of samples
• What sample processing being performed
• What your equipment can handle

Single tubes
96 well plate
384 well plate
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Equipment in a genomics lab

• What you need to process a large genomic / EST
  library
• Sample Preparation
• Colony picking
• DNA extraction
• PCR / sequencing reaction
• Analysis
• Sequencing
• Arraying
• SNP

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Genetix QPix colony picker

• Picks bacterial, yeast and phage
• Picks on basis of size, colour
• Compatible with 96, 384 and deep well plates

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How colony picker works
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Equipment in a genomics lab

• What you need to process a large genomic / EST
  library
• Sample Preparation
• Size of sample plate
• Colony picking
• DNA extraction
• PCR / sequencing reaction
• Analysis
• Sequencing
• Arraying
• SNP

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Liquid handling robots

• Eight tip robot with gripper arm and 4 tip robot
• Heated and cooled stations
• Integrated shaker and fluorescence plate reader
• Can use 96 / 384 / 1536 well plates
• Automate most bench-top assays

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Liquid handling robots

• Protocols that can be performed
• DNA extraction
• DNA quantification
• PCR
• Sequencing reactions
• Enzyme reactions

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Equipment in a genomics lab

• What you need to process a large genomic / EST
  library
• Sample Preparation
• Size of sample plate
• Colony picking
• DNA extraction
• PCR / sequencing reaction
• Analysis
• Sequencing
• Arraying
• SNP

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Principals of sequencing

• Based on incorporation of chain terminator
  nucleotides
• Nucleotides labelled with radioactivity or
  fluorescent dye
• Reaction contains a mixture of nucleotides
• Labelled nucleotide is incorporated at every base
• Products separated on a gel or capillary
• Sequence read according to length of product

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• Anneal primer to template DNA

• Add mixture of nucleotides, enzyme

• Nucleotides incorporated

C
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• Products separated based on length with 1bp
  resolution
• Fluorescent label detected giving sequence

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Capillary Sequencer

• 8 capillary sequencer
• Sequencing runs up to 1Kb
• Run up to 96 reactions in one run
• Fragment analysis

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How capillary sequencer works
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Equipment in a genomics lab

• What you need to process a large genomic / EST
  library
• Sample Preparation
• Size of sample plate
• Colony picking
• DNA extraction
• PCR / sequencing reaction
• Analysis
• Sequencing
• Arraying
• SNP

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Arraying

• Print samples onto a surface
• Macroarrays - large spots onto nylon membranes
• Microarraying small spots onto glass slides

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Biorobotics TASII microarrayer

• Produce both macroarrays and microarrays
• Prints 108 slides per run
• gt50 000 spots per slide, spots lt90µm
• Can produce protein / antibody arrays

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Equipment in a genomics lab

• What you need to process a large genomic / EST
  library
• Sample Preparation
• Size of sample plate
• Colony picking
• DNA extraction
• PCR / sequencing reaction
• Analysis
• Sequencing
• Arraying
• SNP

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SNP analysis

• SNPs single nucleotide polymorphism
• Single base pair change at a specific locus
• Extremely frequent (1 per lt500 bp)
• Can cause phenotypic changes
• Used in
• Association studies
• Mapping
• Identification

TCGAAATGCATGCGCATGATT
Allele 1
TCGAAATGCATGCGCGTGATT
Allele 2
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Detection of SNP by primer extension
TCGAAATGCATGCGCGTGATT
TCGAAATGCATGCGCATGATT
Anneal primer
TTACGTACGCG
TTACGTACGCG
TCGAAATGCATGCGCATGATT
TCGAAATGCATGCGCGTGATT
polymerase ddNTPs
TTACGTACGCGT
TTACGTACGCGC
TCGAAATGCATGCGCATGATT
TCGAAATGCATGCGCGTGATT
Analyse extension products
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Automated analysis of SNPs