BUSRP PI meeting

6/11/2013

Stefano MontiBioinformatics and Molecular Modeling Core

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

Normal effect of PN

Ctl-MODMSO

PXR-MODMSO

PXR-MOPN

Ctl-MOPN

Effects of PNbackground of reduced PXR

Background :Role of PXR in

normal homeostasis

Effects of PNBackground also changing

PN: PregnenoloneMO: Morpholino

Project 5 Study design

4 sampleseach

Testing the effect of pregnenolone in normal and PXR knockdown zebrafish

Daniel Gusenleitner, Francesca Mulas

641

2

374

18

FastQC

CutAdapt

FastQC

Tophat 2

BamQC

Cufflinks

HtSeq

edgeR

Diff

eren

tial

Expr

essi

on

Data processing workflow

Daniel Gusenleitner, Francesca Mulas

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

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

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