Applied Genomics Technology Center. DNA mRNA Protein transcriptiontranslation DNA isolation DNA...
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Transcript of Applied Genomics Technology Center. DNA mRNA Protein transcriptiontranslation DNA isolation DNA...
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