Web site for step-by-step Instructions

Slides:

Advertisements

Similar presentations

Microarray Technique, Analysis, and Applications in Dermatology Jennifer Villaseñor-Park 1 and Alex G Ortega-Loayza 2 1 Department of Dermatology, University.

Advertisements

Lecture 7 Gene Structure and Transposable Elements Gene structure Gene families Repetitive DNA including transposons Organelle genomes Reading: Chapter.

20,000 GENES IN HUMAN GENOME; WHAT WOULD HAPPEN IF ALL THESE GENES WERE EXPRESSED IN EVERY CELL IN YOUR BODY? WHAT WOULD HAPPEN IF THEY WERE EXPRESSED.

DNA microarray example: –As a scientist, you are interested in the differences in expression patterns between normal human cells and cancer cells –A DNA.

DNA Microarray: A Recombinant DNA Method. Basic Steps to Microarray: Obtain cells with genes that are needed for analysis. Isolate the mRNA using extraction.

Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes Mark Schena, Dari Shalon, Renu Heller, Andrew Chai, Patrick O. Brown,

DNA Arrays …DNA systematically arrayed at high density, –virtual genomes for expression studies, RNA hybridization to DNA for expression studies, –comparative.

RNA-Seq An alternative to microarray. Steps Grow cells or isolate tissue (brain, liver, muscle) Isolate total RNA Isolate mRNA from total RNA (poly.

Information Aspects of Nucleic Acids Measurement Technologies Description of nucleic acid measurement technologies Algorithmic, optimization, data analysis.

1 April, 2005 Chapter C4.1 and C5.1 DNA Microarrays and Cancer.

Introduce to Microarray

Urbana, IL| MAY 22, 2009 Anatomical Localization BeeSpace 5 th Annual Workshop Institute for Genomic Biology University of Illinois at Urbana-Champaign.

Genome Sequencing & App. of DNA Technologies Genomics is a branch of science that focuses on the interactions of sets of genes with the environment. –

Chapter 5 Nucleic Acid Hybridization Assays A. Preparation of nucleic acid probes: 1. Labeling DNA & RNA - Nick Translation - Random primed DNA labeling.

How do you identify and clone a gene of interest? Shotgun approach? Is there a better way?

CDNA Microarrays MB206.

Data Type 1: Microarrays

Gene Expression Data Qifang Xu. Outline cDNA Microarray Technology cDNA Microarray Technology Data Representation Data Representation Statistical Analysis.

Genome Sequencing & App. of DNA Technologies Genomics is a branch of science that focuses on the interactions of sets of genes with the environment. –

Remember the limitations? –You must know the sequence of the primer sites to use PCR –How do you go about sequencing regions of a genome about which you.

Expression of the Genome The transcriptome. Decoding the Genetic Information  Information encoded in nucleotide sequences contained in discrete units.

Plasmids Continued Once we insert the plasmid into the bacteria how do we know its in the bacteria and has the the right gene in it?

Gene expression. The information encoded in a gene is converted into a protein  The genetic information is made available to the cell Phases of gene.

Microarray Technology. Introduction Introduction –Microarrays are extremely powerful ways to analyze gene expression. –Using a microarray, it is possible.

Genetic Testing Amniocentesis Until recently, most genetic testing occurred on fetuses to identify gender and genetic diseases. Amniocentesis is one technique.

Disease Diagnosis by DNAC MEC seminar 25 May 04. DNA chip Blood Biopsy Sample rRNA/mRNA/ tRNA RNA RNA with cDNA Hybridization Mixture of cell-lines Reference.

Pedagogical Objectives Bioinformatics/Neuroinformatics Unit Review of genetics Review/introduction of statistical analyses and concepts Introduce QTL.

Genes and Chips. Genes….  The proper and harmonious expression of a large number of genes is a critical component of normal growth and development and.

Transcriptome What is it - genome wide transcript abundance How do you obtain it - Arrays + MPSS What do you do with it when you have it - ?

Microarray: An Introduction

Detecting DNA with DNA probes arrays. DNA sequences can be detected by DNA probes and arrays (= collection of microscopic DNA spots attached to a solid.

Simple-Sequence Length Polymorphisms

Part 3 Gene Technology & Medicine

Genomics A Systematic Study of the Locations, Functions and Interactions of Many Genes at Once.

Immunohistochemistry and in situ hybridization allow researchers to pinpoint the expression of their protein and nucleic acid targets, respectively.

Fig. 1. In situ hybridization analysis for detecting endogenous mBest1 transcript in whole-brain region. In situ hybridization results from coronal (top.

Gene Expression Analysis

Redefining DNA Microarrays

Expression of the Genome

Genomics is an interdisciplinary field of science within the field of

Functional Genomics in Evolutionary Research

 The human genome contains approximately genes.  At any given moment, each of our cells has some combination of these genes turned on & others.

Dr T-J’s Minilecture Chapter 12.

DNA Tools & Biotechnology

Lecture 11 By Shumaila Azam

Example of a DNA Array (note green, yellow red colors; also note that only part of the total array is depicted)

by Leighton J. Core, Joshua J. Waterfall, and John T. Lis

محاضرة عامة التقنيات الحيوية (هندسة الجينات .. مبادئ وتطبيقات)

Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states by Thu-Hang Pham, Christopher.

DNA Tools & Biotechnology

Correlation of log-transformed signal intensity from two Affymetrix microarray hybridizations using platelet RNA. Plotted are those probesets with an average.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

DNA Chip Data Interpretation Tools: Genmapp & Dragon View

High-Resolution Profiling of Histone Methylations in the Human Genome

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters by Pascal Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke-Andersen,

Microarray Techniques to Analyze Copy-Number Alterations in Genomic DNA: Array Comparative Genomic Hybridization and Single-Nucleotide Polymorphism Array

High-Resolution Profiling of Histone Methylations in the Human Genome

Volume 16, Issue 8, Pages (August 2016)

Genome-wide analysis of p53 occupancy.

Translational control in endothelial cells

Emergence of a New Gene from an Intergenic Region

Gene Expression Analysis

Microarrays: biotechnology's discovery platform for functional genomics Mark Schena, Renu A Heller, Thomas P Theriault, Ken Konrad, Eric Lachenmeier,

Chromosome 8 cDNA microarray gene expression profile of the amplified regions of 8p11–12 in SUM-44, -52, and -225 cells versus MCF10A HME control cells.

Gene Amplification as a Developmental Strategy

Data Type 1: Microarrays

by Leighton J. Core, Joshua J. Waterfall, and John T. Lis

Mapping of Small RNAs in the Human ENCODE Regions

Presentation transcript:

Web site for step-by-step Instructions http://mdcune.psych.ucla.edu/modules/qtl

Web site for step-by-step Instructions http://mdcune.psych.ucla.edu/modules/qtl SPSS Instructions 8-20-09(.pdf) SPSS_QTL Data_Template

Example data only—yours will be different.

Not yer data! Variables Controlled by Regression

Example data only—yours will be different.

Web site for step-by-step Instructions http://mdcune.psych.ucla.edu/modules/qtl Using GeneNetwork_QTL SPSS_QTL Data_Template

Web site for step-by-step Instructions http://mdcune.psych.ucla.edu/modules/qtl BXD_geno Markers032609

Defining a Peak and looking for SNPs Peak is defined by a drop of 4.6 in the LRS from maximum This is about 1 log unit Pay particular attention to SNPs in our peak or region of interest

Clickable track to corresponding display in UCSC Genome Browser. Each Small colored box represents a known gene Likelihood ratio statistic SNP Density Peak 65-85 Megabases

Web site for step-by-step Instructions http://mdcune.psych.ucla.edu/modules/qtl Using UCSC Genome Browser

Clickable track to corresponding display in UCSC Genome Browser.

Clickable genes!

For Gabarapl1, Dr.G’s gene.

Gene Chips DNA microarrays Can use fluorescent cDNAs (mRNAs or RNAs) as probes. Yield the pattern of gene expression across 2 different conditions. Can examine many (thousands) of genes at once. Does not give cell-by-cell resolution.

Gene Chip Animation http://www.bio.davidson.edu/courses/genomics/chip/chip.html

Web site for step-by-step Instructions http://mdcune.psych.ucla.edu/modules/qtl Using the Allen Brain Atlas

In situ hybridization Finding out which cell(s) express a gene by probing for mRNA. Probes to mRNA can be made of antisense DNA or RNA (sense is control). Probes are labeled. Probes hybridize with specific mRNAs being made in a cell. Can only examine expression of one or two genes at a time.

Web site for step-by-step Instructions http://mdcune.psych.ucla.edu/modules/qtl Using Entrez Gene

Web site for step-by-step Instructions http://mdcune.psych.ucla.edu/modules/qtl Using PubMed