Applied Genomics Technology Center

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Applied Genomics Technology Center
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DNA mRNA
Protein
Protein purification Enzymology Immunohistochemist
ry Western Blot analysis Protein microarrays Ab
microarrays Yeast 2 hybrid analysis
DNA isolation DNA sequencing Genotyping Gene
linkage mapping
RNA isolation Expression analysis
Microarrays QRT-PCR
www.AGTC.med.wayne.edu
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Illumina GAII
IPAR
2 - 4TB
Primary Server Illumina Pipeline
Failover Reanalysis Server
Testbed Server
3x R900 64GB RAM
30TB Direct Attached Storage
30TB Direct Attached Storage
10TB Direct Attached Storage
48TB NAS
Backup Mirror (CIT)
User Data Delivery Downstream Analysis eg
Genomatix
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Whole Genome Maps
from the base pair
to the chromosome
Ruden Lab, IEHS
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Synonymous/Non-synonymous polymorphism
Coverage/deletion maps
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Krawetz Lab
Histone Locations Relative to All Promoters
Histone Locations Relative to Alu/B1 Repeats
Permuted Control
2kbase
Full ALU Repeat Length
Downstream (Genic)
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Small RNA Digital Gene Expression
Most of the reads dont correspond to known
sncRNAs
Peak of intergenic location found with high
representation in all 3 libraries and showing
miRNA potential (hairpin)

• 4 manuscripts in preparation using Solexa data
• At the end of spermatogenesis the DNA is not
  methylated
• small RNAs may transfer the information
  for methylation
• Discovery of a new class of small,
  non-coding RNAs of unknown function

Krawetz Lab
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Ruden Bee Project
Genetics and Genomics of Social Behavior
Phase I funding for a Glue Grant PI Gene
Robinson (UIUC) 27 Co-PIs Pilot Project
Genome sequencing and bisulfite sequencing of
European honey bees and Africanized killer
bees (funded by WSU OVPR and Ob/Gyn) Progress 4
Libraries have been established and about 50 of
the sequencing is complete 3 lanes of Sequencing
and 1 lane of BS-Seq have been analyzed for each
strain Results 9 Loci on chromosome 1 have gt51
mC ratios (EurAfr) 43 loci on chromosome 1 have
gt51 mC ratios (AfrEur)
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Ruden Bee Project Preliminary Results

• FMRFamide Receptor
• neuropepetide receptor
• Methylated in Africanized bees in three regions
• Involved in
• agression in mice (PMID 7630503)
• defense behavior in snails (PMID 2067975)
• Kainate Glutamate Receptor
• Methylated in Euopean bees in two regions
• Kainate induces aggression in mice (PMID
  15123017)
• GAT1
• Methylated in African bees
• Deletion of GAT1 in mice causes reduced
  agression (PMID 17183588)

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Ruden Bee Project Future Experiments
How much DNA methylation is Genetic and how
much is Environmentally induced? Next
step Cross Fostering Experiment Killer
bee soldiers in European hives European
bee soldiers in Killer bee hives NIH Pioneer
Award PI Gene Robinson
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Human DBS DNA Methylation
DBS from 28 children with varying Pb levels was
obtained from MDCH (3 to 16 ug/dL) PB levels
(CDC) High10 ug/dL Low 3
ug/dL Illumina Whole Genome Methylation Arrays
(27,576 CpG islands) Results Several loci
have mC with significant correlations to Pb
exposure 5 genes involved in
myelination (Mbp, Edg2, Mag, Pmp22, and Ugt8)
6 genes involved in growth factor signaling
(FGfr1, Gzd3, Erbb3, Mag, Pmp22
and Ugt 8) All of these genes have
prior evidence of differential expression in
human postmortem brains from mood
disorder subjects (Le-Niculescu et al., 2009)
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Human DBS DNA Methylation