Topic intro slides More complete coverage of components involved in gene expression More information...

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Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip do? -limitations to expression technologies Datasets that have been produced thus far

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Transcript of Topic intro slides More complete coverage of components involved in gene expression More information...

Page 1: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Topic intro slides

More complete coverage of components involved in gene expression

More information on expression technologies-what would the ideal chip do?-limitations to expression technologies

Datasets that have been produced thus far

Page 2: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Genes and Gene ExpressionTechnologyDisplay of Expression Information

Page 3: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Genomic DNA

Promoter Protein coding sequence Terminator

What is a gene?

Page 4: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

rRNAtRNAmRNAsnRNAsRNA

Genomic DNA

Types of genes

Page 5: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

TFIIB

RNAPII

TFIIATFIID

TFIIH TFIIF

Mediator

TFIIE

Activators

How are Genes Regulated? DNA-binding Activators Are Key To Specific Gene Expression

Gene

Chromatin modification complexes

Transcription initiation apparatus

Page 6: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

TFIIB

RNAPII

TFIIATFIID

TFIIH TFIIF

Mediator

TFIIE

Activators

How are Genes Regulated? DNA-binding activators are key, but there are additional factors

Gene

Chromatin modification complexes

Transcription initiation apparatus activators

repressorscoactivatorscorepressorstranscription apparatuschromatin factorsRNA processingRNA transportRNA degradation

Page 7: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Activators

Genome-wide Gene Expression (mRNA) can be Measured with DNA Microarrays

GeneRNAPIITFIIH

Transcription apparatus

mRNA

mRNAlabel

hybridization ATGC

TACG

Page 8: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.
Page 9: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Some Additional Numbers

Yeast:6200 genes~200 transcriptional regulators

Human:30,000 - 50,000 genes~1700 transcriptional regulators>100 cell types

Page 10: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Genes and Gene ExpressionTechnologyDisplay of Expression Information

Page 11: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Coated glass microarrays

In situ oligonucleotide synthesis arrays

DNA array technology

Page 12: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Hybridization and Scanning—Glass slide arrays

- Prepare Cy3, Cy5- labeled ss cDNA

- Hybridize 600 ng of labeled ss cDNA to glass slide array

- Scan

Page 13: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Glass Slide DNA Arrays

• Large DNA molecules, PCR products, oligonucleotides, and proteins can be arrayed

• Typically non-specific binding to glass or coated surfaces

• High quality coated slides commercially available

Page 14: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Cartesian PixSys 5500 withquill printing technology

• 3 x 1 inch microscope slides, specially coated with amino groups• 50 slides/ bed• Up to 32 pins (quills)• 10,000 spots/slide• Spots are 100-200 µm in diameter• Hybridization volumes: 20-100ul

Page 15: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Array Scanning

Laser based - fluorescent emission

Page 16: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Spot Finding

Page 17: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Affymetrix high density oligonucleotide arrays: S. cerevisiae• Oligonucleotides synthesized in situ using light- directed, solid phase combinatorial chemistry

• 6181 ORFs + controls for alignment and normalization

• each ORF: 20 perfect match 25-mers (PM)20 single base mismatch partners (MM)

• mRNA signal = average of differences (PM-MM)

• average number of ORF mRNAs detected = 5460

• dynamic range = 0.1 - 100 mRNA molecules/cell

Page 18: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Hybridization and Scanning—Affymetrix arrays

Biotin-labeled cRNA target #1

- hybridize 10-40 g of cRNA to Affymetrix array

- Wash and scan

Compare data sets #1 & #2

Biotin-labeled cRNA target #2

- Wash and scan

Page 19: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Rosetta

Ink-jet printingNon-proprietary phosphoamidite oligonucleotide synthesis29,000 oligos/1X3 inches40-60 nucleotides/oligo

More information: Hughes et al., Nature Biotechnology 2001

Page 20: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Genes and Gene ExpressionTechnologyDisplay of Expression Information

Page 21: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

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Mcm1/Fkh2/Ndd1

Ace2, Swi5, Mcm1

1 3.5 >5

1/3 1 3

Yeast Cell Cycle Gene Expression Program

Spellman et al. and Cho et al., 1998

800 Genes

Page 22: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

>9 >6 >3 1:1 >3 >6 >9Fold repression Fold inductionGenomic Reprogramming in Response to Oxidant010204060120minutes One-third of genome expression is transiently reprogrammed6218 genes

ROS response

Page 23: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

600 Conditions/Mutations

620

0 G

ene

s

Single-gene MutationsEnvironment

Exercising the Genome

Page 24: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

Visualization: Relative vs. absolute expression

Page 25: Topic intro slides More complete coverage of components involved in gene expression More information on expression technologies -what would the ideal chip.

A comparative study of access topologies for chip-level ... · macro-scale systems to analyze access topologies for intra-chip and inter-chip communication. More specifically, our

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More on TF Motif Finding ChIP-chip / seq

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ChIP-Seq of transcription factors predicts absolute and differential … · ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem

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2: Large-Scale 1 / 42 1 Large!. 2: Large-Scale 2 / 42 High throughput technologies: Sequencing Gene expression profiling Chip-CHIP and tiling arrays Whole.

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Chromatin Immunoprecipitation and the Chip on Chip technique. Fredrik Fagerström Billai B E A- Core Facility for Bioinformatics and Expression Analysis.

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Chapter 4 Expression Operators - Tun Hussein Onn …author.uthm.edu.my/uthm/www/content/lessons/4811/le… ·  · 2014-09-29What is Expression? 5 Expression Combination or more than

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Cutting Corners - Boston University Physicsphysics.bu.edu/~redner/talks/cutting-corners.pdf · Cutting Corners Results: ... preferentially chip prominent corners; chip more than 1

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Introduction to Microarray Analysis - uni-mainz.de · Introduction to Microarray Analysis ... multiplex lab-on-chip ... { DNA microarrays Microarray experiment gene expression quanti

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2: Large-Scale Large!. 2: Large-Scale High throughput technologies: Sequencing Gene expression profiling Chip-CHIP and tiling arrays Whole genome yeast.

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Chapter 1: Expressions, Equations, and Functions · Write an algebraic expression for each verbal expression. a. a number t more than 6 The words more than suggest addition. Thus,

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What is an “SoC”? SoC = SOC = System on Chip = System on a Chip Wider use: a Chip that implements a Complete System More common use: a Chip with one or.

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Figure - people.vcu.edu · Web viewIf no promoter site exists, HIF-1a can not possible impact Apold 1 gene expression. To do so, I obtained the HIF-1a ChIP-Seq/Homer. ChIP sequenceing

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Comparative analysis of gene expression profiles in normal ......expression profiling of NFH articular cartilage was carried out by Agilent Human 4x44K Gene Expression Microarray chip.

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ChIP-seq - Expression NetworksThe ultimate goal of ChIP-seq experiments is to measure ... We have not yet covered (3) in this course, but it will be your challenge for the next decade!

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Computer)Architecture)101) · 2012-09-02 · Flash‘Based)SSD)Architecture) chip chip chip … chip chip chip … chip chip chip … chip chip chip … Read Write Trim Logical address

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