Genomics

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Genomics
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Complete Genomes in The Public DataBases gt100
Non-Eukaryotes Eukaryotes Leishmania
257 Kb 79 orfs Plasmodium falciparum I
947 Kb 205 orfs Plasmodium falciparum
I 1,060 Kb 220 orfs Guillardia theta
551 Kb 464 orfs Arabidopsis thaliana
115,428 Kb 25,498 orfs Oryza (sativa L. ssp.
Indica) 420,000 Kb 50,000 orfs Oryza (sativa
ssp. Japonica) 420,000 Kb 50,000
orfs Saccharomyces cerevisiae 12,069 Kb
6,294 orfs Schizosaccharomyces pombe 14,000 Kb
6,824 orfs Caenorhabditis elegans 97,000
Kb 19,099 orfs Drosophila melanogaster 137,000
Kb 14,100 orfs Mouse Musculus
3,000,000Kb 50,000 orfs Homo sapiens
3,000,000Kb 50,000 orfs
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SEQUENCING (according to Sanger et al.)

1. Annealing and elongation
2. Termination

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Manual Sequencing
1 2 3
a g c t a g c t a g c t
4 lanes / sample 10 samples / gel 200-400 bases
long
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Dye Terminator Sequencing
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Sequencing
DNA template
primers
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Dye Terminator Cycle Sequencing
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Primer Walking
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Shotgun Sequencing
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Single Nucleotide Polymorphism (SNP)

• Single nucleotide polymorphisms (SNPs), i.e.,
  single nucleotide base substitutions in gene
  sequences, account for 85 of the genetic
  variability in humans.
• This variability quite often accounts for
  differences in individuals' susceptibility to
  diseases and varying response to therapeutics.
• SNPs also have high utility in discovery of
  novel candidate genes through high resolution
  mapping

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SNaPshotTM Multiplex Kit Work Flow
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SNaPshotTM Multiplex Kit Single Base Extension
ddGTP ddCTP ddUTP ddATP
Interrogation target
G
CCATGACTGATTCC
NNNNNNAGCCTGGTACTGACTAAGGCNNNNNNN
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SNaPshotTM Multiplex Kit Single Base Extension
Extends and Terminates Primer
ddCTP ddUTP ddATP
Interrogation target
G
CCATGACTGATTCC
NNNNNNAGCCTGGTACTGACTAAGGCNNNNNNN
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SNaPshot reaction heterozygote
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Sub
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DNA micro-arrays
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DNA Microarray (Filter)
Apoptosis/DNA Repair
Oncogenes/Cell cycle
Signal Transduction
House Keeping
Growth Factors
Transcrption Factors
Receptors
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Glass DNA Chip
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Photolithography
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