Applied Genomics Technology Center

DNA mRNA Proteintranscription translation

DNA isolationDNA sequencingGenotypingGene linkage mapping

Protein purificationEnzymologyImmunohistochemistryWestern Blot analysisProtein microarraysAb microarraysYeast 2 hybrid analysis

RNA isolationExpression analysis Microarrays QRT-PCR

www.AGTC.med.wayne.edu

Illumina GAII

2 - 4

TB

IPAR

Primary ServerIllumina Pipeline

Failover &Reanalysis Server Testbed Server

30TBDirect Attached

Storage

30TBDirect Attached

Storage

10TBDirect Attached

Storage48TBNAS

Back

up

Mirr

or (C

&IT

)

3x R90064GB RAM

User Data Delivery & Downstream Analysis eg Genomatix

Whole Genome Mapsfrom the base pair to the chromosome

Ruden Lab, IEHS

Coverage/deletion maps Synonymous/Non-synonymous polymorphism

Histone Locations Relative to All Promoters

Permuted Control

Histone Locations Relative to Alu/B1 Repeats

Full ALU Repeat Length Downstream (Genic)

2kbase

Krawetz Lab

Small RNA Digital Gene Expression

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

Library Alignments # SequencesAS062 ≤10 625582

  Unique 552332AS064 ≤10 225563

  Unique 110805AS066 ≤10 528475

  Unique 285078

Peak of intergenic location found with high representation in all 3 libraries and showing miRNA potential (hairpin)

Most of the reads don’t correspond to known sncRNAs

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 complete3 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 stepCross 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