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Applied Genomics
Technology Center
DNA
transcription
DNA isolation
DNA sequencing
Genotyping
Gene linkage mapping
mRNA
translation
RNA isolation
Expression analysis
Microarrays
QRT-PCR
www.AGTC.med.wayne.edu
Protein
Protein purification
Enzymology
Immunohistochemistry
Western Blot analysis
Protein microarrays
Ab microarrays
Yeast 2 hybrid analysis
IPAR
2 - 4TB
Illumina GAII
3x R900
64GB RAM
Backup
Mirror (C&IT)
48TB
NAS
Primary Server
Illumina Pipeline
Failover &
Reanalysis Server
30TB
Direct Attached
Storage
30TB
Direct Attached
Storage
Testbed Server
10TB
Direct Attached
Storage
User Data Delivery & Downstream Analysis eg Genomatix
Whole Genome Maps
from the base pair
Ruden Lab, IEHS
to the chromosome
Coverage/deletion maps
Synonymous/Non-synonymous polymorphism
Krawetz Lab
Histone Locations Relative
to All Promoters
Histone Locations Relative
to Alu/B1 Repeats
Permuted Control
2kbase
Downstream (Genic)
Full ALU Repeat Length
Small RNA Digital Gene Expression
Most of the reads don’t correspond to known sncRNAs
Library
AS062
AS064
AS066
Alignments
≤10
Unique
≤10
Unique
≤10
Unique
# Sequences
625582
552332
225563
110805
528475
285078
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
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 >5:1 mC ratios (Eur:Afr)
43 loci on chromosome 1 have >5:1 mC ratios (Afr:Eur)
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)
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
Human DBS DNA Methylation
DBS from 28 children with varying Pb levels was obtained from MDCH (3 to 16 ug/dL)
PB levels (CDC)
High:10 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)
Human DBS DNA Methylation
CpG
Corr
P-value
1
-0.52
0.005
2
-0.54
0.003
overall
0.000015