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

Slides:

Advertisements

Similar presentations

IMGS 2012 Bioinformatics Workshop: RNA Seq using Galaxy

Advertisements

Processing of miRNA samples and primary data analysis

Simon v2.3 RNA-Seq Analysis Simon v2.3.

Peter Tsai Bioinformatics Institute, University of Auckland

DEG Mi-kyoung Seo.

RNAseq analysis Bioinformatics Analysis Team

Transcriptomics Jim Noonan GENE 760.

RNA-seq Analysis in Galaxy

High Throughput Sequencing

mRNA-Seq: methods and applications

Before we start: Align sequence reads to the reference genome

NGS Analysis Using Galaxy

An Introduction to RNA-Seq Transcriptome Profiling with iPlant

RNA-Seq Visualization

Big Data Network Genomics Network Inference and Perturbation to Study Chemical-Mediated Cancer Induction Stefano Monti Section of Computational.

Bioinformatics and OMICs Group Meeting REFERENCE GUIDED RNA SEQUENCING.

PXR in zebrafish: preliminary RNA-Seq analysis. SRP Project 5: Developmental Toxicity of non-Dioxin-like PCBs and Chemical Mixtures John Stegeman, PI.

Transcriptome analysis With a reference – Challenging due to size and complexity of datasets – Many tools available, driven by biomedical research – GATK.

RNAseq analyses -- methods

RNA-Seq Analysis Simon V4.1.

Transcriptome Analysis

Eran Yanowski, Eran Hornstein’s: Monitor drug impact on the transcriptome of mouse beta cells (primary and cell-line) using Transeq/RNA-Seq Report.

Introductory RNA-seq Transcriptome Profiling. Before we start: Align sequence reads to the reference genome The most time-consuming part of the analysis.

Introduction to RNA-Seq

The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop RNA-Seq using the Discovery Environment And COGE.

Introduction To Next Generation Sequencing (NGS) Data Analysis

RNA-Seq Assembly 转录组拼接唐海宝基因组与生物技术研究中心 2013 年 11 月 23 日.

Next Generation Sequencing pipeline: a joint LONI – BIRN [UCLA – UCI] collaborative project F. Macciardi – March 16, 2011.

Contribution of Epigenetic Variation to Expression Changes Among Tissues and Genotypes Steve Eichten – Springer Lab PAG iPlant Workshop 1/17/12.

Introductory RNA-seq Transcriptome Profiling. Before we start: Align sequence reads to the reference genome The most time-consuming part of the analysis.

Galaxy – Set up your account. Galaxy – Two ways to get your data.

RNA-Seq Primer Understanding the RNA-Seq evidence tracks on the GEP UCSC Genome Browser Wilson Leung08/2014.

RNA-Seq Transcriptome Profiling. Before we start: Align sequence reads to the reference genome The most time-consuming part of the analysis is doing the.

Environmental Cancer Genomics from High-Throughput Assays to Prevention Stefano Monti Art beCAUSE consortium meeting 8/4/2015 – 9/1/2015.

Introduction to RNAseq

Geuvadis achievements and contributions Robert Häsler, functional genomics.

( ) 2.2 FC autism control FGR1OP2. ( ) 1.4 FC autism control SMAD2.

Sushi – An exquisite recipe for NGS data analysis Hubert Rehrauer & Masaomi Hatakeyama Supporting User for SHell-script Integration.

ANALYSIS OF GENE EXPRESSION DATA. Gene expression data is a high-throughput data type (like DNA and protein sequences) that requires bioinformatic pattern.

RNA-seq: Quantifying the Transcriptome

The iPlant Collaborative

No reference available

First of all: “Darnit Jim, I’m a doctor not a bioinformatician!”

Canadian Bioinformatics Workshops

Overview of Genomics Workflows

Canadian Bioinformatics Workshops

Canadian Bioinformatics Workshops

Canadian Bioinformatics Workshops

Arrays How do they work ? What are they ?. WT Dwarf Transgenic Other species Arrays are inverted Northerns: Extract target RNA YFG Label probe + hybridise.

RNA-Seq with the Tuxedo Suite Monica Britton, Ph.D. Sr. Bioinformatics Analyst September 2015 Workshop.

Centralizing Bioinformatics Services: Analysis Pipelines, Opportunities, and Challenges with Large- scale –Omics, and other BigData High-Performance Computing.

Misleading bioinformatics: Mistakes, Biases, Mis-interpretations and how to avoid them Festival of Genomics 2017 Course Exercise Material:

Bioinformatics core facility, OUS/UiO

An Introduction to RNA-Seq Data and Differential Expression Tools in R

Placental Bioinformatics

Cancer Genomics Core Lab

Dr. Christoph W. Sensen und Dr. Jung Soh Trieste Course 2017

RNA-Seq analysis in R (Bioconductor)

Tutorial 6 : RNA - Sequencing Analysis and GO enrichment

S1 Supporting information Bioinformatic workflow and quality of the metrics Number of slides: 10.

High-Throughput Analysis of Genomic Data [S7] ENRIQUE BLANCO

Canadian Bioinformatics Workshops

Kallisto: near-optimal RNA seq quantification tool

The DHX15–CMTR1 interaction inhibits translation of a subset of genes.

Supplementary fig 1: Video showing heart function in zebrafish embryos targeted with morpholino oligonucleotides to reduce Brn-3a and Brn-3b compared with.

Premature Termination Codon Read-Through in the ABCC6 Gene: Potential Treatment for Pseudoxanthoma Elasticum Yong Zhou, Qiujie Jiang, Shunsuke Takahagi,

Sequence Analysis - RNA-Seq 2

AhR activation alters gene expression in human monocyte-derived DCs

The Technology and Biology of Single-Cell RNA Sequencing

RNA-Seq Data Analysis UND Genomics Core.

Presentation transcript:

BUSRP PI meeting 6/11/2013 Stefano Monti Bioinformatics 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-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

FastQC CutAdapt FastQC Tophat 2 BamQC Cufflinks HtSeq edgeR Differential Expression 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