1. BUSRP PI meeting 6/11/2013 Stefano Monti Bioinformatics and Molecular Modeling Core

2. Progress Report  Carcinogenicity biomarker development Work (partially) supported by BUSRP admin supplement Manuscript accepted to PLoS ONE Gusenleitner D, Auerbach S, …, Sherr D, Monti S.  Project 5 RNA-seq data processed and analyzed Interpretation of results ongoing  Project 4 RNA-seq data processed and analysis ongoing

3. Normal effect of PN Ctl-MO DMSO PXR-MO DMSO PXR-MO PN Ctl-MO PN Effects of PN background of reduced PXR Background : Role of PXR in normal homeostasis Effects of PN Background also changing PN: Pregnenolone MO: Morpholino Project 5 Study design 4 samples each Testing the effect of pregnenolone in normal and PXR knockdown zebrafish Daniel Gusenleitner, Francesca Mulas

4. 641 2 374 18 FastQC CutAdapt FastQC Tophat 2 BamQC Cufflinks HtSeq edgeR Differential Expression Data processing workflow Daniel Gusenleitner, Francesca Mulas

5. Project 4 RNASeq project outline  Organism: Killifish (WT and PCB resistant)  Acute exposure of fertilized embryos to PCB 153  Killifish embryos (10 days post-fertilization) were exposed to PCB-153 or DMSO (vehicle) for 6 hrs, then used for RNA preparation  Only the high concentration of PCB 153 was analyzed by RNA-seq.  Four treatment groups (n=5/group): Scorton Creek (SC) - DMSO (vehicle) Scorton Creek (SC) - PCB-153 New Bedford Harbor (NBH) - DMSO (vehicle) New Bedford Harbor (NBH) - PCB-153 Vinay Kartha, Daniel Gusenleitner, Francesca Mulas

6. Project 4 RNASeq project goals  To identify genes whose expression is altered after acute exposure to PCB-153  To identify population-specific differences in responsiveness - number and identity of genes altered  Detect possible splice variants at any four of the AHR loci, and whether there are any population/treatment-specific differences in variants detected Vinay Kartha, Daniel Gusenleitner, Francesca Mulas

7. Progress Report  Ran RNASeq pipeline on all 20 samples Includes QC reports on raw, processed and aligned read data  Current: Generating count data to be used for pairwise differential expression analyses: PCB vs DMSO (SC population) PCB vs DMSO (NBH population)  Next: Look for gene expression signatures that are unique to a given population Vinay Kartha, Daniel Gusenleitner, Francesca Mulas