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Microarray

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DNA microarrays, also known as DNA chips, allow simultaneous measurement of gene expression levels for every gene in a genome. They detect mRNA levels by hybridizing cDNA to arrays of gene probes spotted on glass slides or other surfaces. Differences in gene expression between cell types or conditions can be measured and analyzed to answer biological questions.

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DNA Microarrays Ms.ruchi yadav lecturer amity institute of biotechnology amity university lucknow(up)
Gene expression A human organism has over 250 different cell types (e.g., muscle, skin, bone, neuron), most of which have identical genomes, yet they look different and do different jobs It is believed that less than 20% of the genes are‘expressed’ (i.e., making RNA) in a typical cell type Apparently the differences in gene expression is what makes the cells different
Microarray
Microarray
Microarray
Gene Expression Patrick Schmid
Uses and Applications
Microarrays: Universal Biochemistry Platforms Peptides Proteins Carbohydrates Lipids Small molecules DNA
Some questions for the golden age of genomics How gene expression differs in different cell types? How gene expression differs in a normal and diseased (e.g., cancerous) cell? How gene expression changes when a cell is treated by a drug? How gene expression changes when the organism develops and cells are differentiating? How gene expression is regulated – which genes regulate which and how?
What is a DNA Microarray? (cont.) Biological Samples in 2D Arrays on Membranes or Glass Slides Cheung et al. 1999
What is a DNA Microarray? Also known as DNA Chip Allows simultaneous measurement of the level of transcription for every gene in a genome (gene expression) Microarray detects mRNA, or rather the more stable cDNA
MICROARRAY TYPES
The Colours of a Microarray GREEN represents Control DNA , where either DNA or cDNA derived from normal tissue is hybridized to the target DNA. RED represents Sample DNA , where either DNA or cDNA is derived from diseased tissue hybridized to the target DNA. YELLOW represents a combination of Control and Sample DNA , where both hybridized equally to the target DNA. BLACK represents areas where neither the Control nor Sample DNA hybridized to the target DNA.
Microarray Steps Experiment and Data Acquisition Sample preparation and labelling Hybridisation Washing Image acquisition Data normalization Data analysis Biological interpretation
I. Target and probe preparation
There are many ways to obtain a labeled target sample. ...GGCUUAAUGAGCCUUAAAAAA...A mRNA TTTTTT...T viral enzyme reverse transcriptase recognizes poly-T bound to poly-A and begins to add complementary DNA nucleotides. The C nucleotides are dyed. A A A G G C T C T T A A G C C ... poly-A tail cDNA target poly-T primer
Hybridization and Data Analysis
Spotted Array Synthesis.
Microarray Experiment
How do we manufacture a microarray? Start with individual genes, e.g. the ~6,200 genes of the yeast genome Amplify all of them using polymerase chain reaction (PCR) “ Spot” them on a medium, e.g. an ordinary glass microscope slide Each spot is about 100 µm in diameter Spotting is done by a robot Complex and potentially expensive task
Robotic spotting
Microarray
DNA Samples on 96 well plates
The PixSys 5500 Arraying Robot (Cartesian Technologies) Vacuum wash station The print head holds up to 32 pins in a 8x4 format Vacuum hold-down platform (50 slide capacity) Robotic arm
Contact Printing
Non Contact Printing InkJet (HP/Canon) technology • 1 drop = 100 picolitres
Microarray
Spotting the Probes on the Microarray 8 X 4 Print Head microarray slide plate with wells holding probes in solution All spots of the same color are made at the same time. All spots in the same sector are made by the same pin.
Using cDNA Microarrays to Measure mRNA Levels ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? Sample 1 Sample 2 Microarray Slide Spots (Probes) Unknown mRNA Sequences (Target)
Extract mRNA ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
Convert to cDNA and Label with Fluorescent Dyes ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
Mix Labeled cDNA ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
Hybridize cDNA to the Slide ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
Excite Dyes with Laser Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G
Scan Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G
Quantify Signals ACCTG...G 7652 138 TTCTG...A 5708 4388 GGCTT...C 8566 765 ATCTA...A 1208 13442 ACGGG...T 6784 9762 CGATA...G 67 239 Sample 1 Sample 2
Patrick Schmid
Microarray
Microarray
Oligonucleotide Microarray Gene chip (DNA chip, Affymetrix chip): Oligonucleotide (20~80-mer oligos) is synthesized either in situ (on-chip) Developed at Affymetrix, Inc. , under the GeneChip® trademark
Affymetrix Chip Each gene has 16 – 20 pairs of probes synthesized on the chip Each pairs of probes have two oligonucleotide – Perfect match (PM, reference seq) ATG…C…TGC (20-25 bases) – Mismatch (MM, one base change) ATG… T …TGC A MM oligo is identical to a PM oligo except that the middle nucleotide (13 th of 25) is intentionally replaced by its complementary nucleotide . The scanned result for a given gene is the average differences between PM and MM signals, over probes
Different Probe Pairs Represent Different Parts of the Same Gene gene sequence Probes are selected to be specific to the target gene and have good hybridization characteristics.
A Probe Set for Measuring Expression Level of a Particular Gene probe pair gene sequence ...TGCAATGGGTCAGAA G GACTCCTATGTGCCT... AATGGGTCAGAA G GACTCCTATGTG AATGGGTCAGAA C GACTCCTATGTG perfect match sequence mismatch sequence probe set probe cell
Affymetrix Chip
The photolithographic method Treat substrate with chemically protected “linker” molecules, creating rectangular array Selectively expose array sites to light deprotects exposed molecules, activating further synthesis Flush chip surface with solution of protected A,C,G,T Binding occurs at previously deprotected sites Repeat steps 2&3 until desired probes are synthesized
Photolithography The mask only allows light to pass to specific features on the chip
Photolithography
Affymetrix chip Photolithographic Approach In-situ synthesis of oligonucleotide
Photolithographic Approach
Patrick Schmid Affymetrix Arrays
Affymetrix GeneChips The black features represent no intensity (no RNA hybridized to the respective probe in the feature). The intensity level from lowest to highest by color is: Dark blue -> Blue -> Light Blue -> Green -> Yellow -> Orange -> Red - > White . More intensity means more RNA bound to a specific feature, which basically means the gene was expressed at a higher level.
Affymetrix GeneChip experiment
Affymetrix GeneChip experiment labeled cRNA randomly fragmented in to pieces anywhere from 30 to 400 base pairs in length The fragmented, Biotin-labeled cRNA is added to the array Anywhere on the array where a RNA fragment and a probe are complimentary, the RNA hybridizes to the probes in the feature. The array is then washed to remove any RNA that is not stuck to an array then stained with the fluorescent molecule that sticks to Biotin (Cy5 conjugated to streptavidin) Lastly, the entire array is scanned with a laser and the information is kept in a computer for quantitative analysis of what genes were expressed and at what approximate level
in-situ synthesised arrays The different methods for deprotection lead to the three main technologies for making in-situ synthesised arrays: Photodeprotection using masks: this is the basis of the Affymetrix® technology. Photodeprotection without masks : this is the method used by Nimblegen and Febit. Chemical deprotection with synthesis via inkjet technology: this is the method used by Rosetta, Agilent and Oxford Gene Technology.
Photodeprotection without masks
Maskless Array Synthesis
NimbleGen Arrays
Microarray Experiment
Cancer and Microarray
* Measuring levels of gene expression * Creating diagnostic tests to predict whether a patient has a genetic predisposition to obesity * Designing Drugs Gene expression and obesity
Reading an array (cont.) Campbell & Heyer, 2003 Block Column Row Gene Name Red Green Red:Green Ratio 1 1 1 tub1 2,345 2,467 0.95 1 1 2 tub2 3,589 2,158 1.66 1 1 3 sec1 4,109 1,469 2.80 1 1 4 sec2 1,500 3,589 0.42 1 1 5 sec3 1,246 1,258 0.99 1 1 6 act1 1,937 2,104 0.92 1 1 7 act2 2,561 1,562 1.64 1 1 8 fus1 2,962 3,012 0.98 1 1 9 idp2 3,585 1,209 2.97 1 1 10 idp1 2,796 1,005 2.78 1 1 11 idh1 2,170 4,245 0.51 1 1 12 idh2 1,896 2,996 0.63 1 1 13 erd1 1,023 3,354 0.31 1 1 14 erd2 1,698 2,896 0.59
Color Coding Tables are difficult to read Data is presented with a color scale Coding scheme: Green = repressed (less mRNA) gene in experiment Red = induced (more mRNA) gene in experiment Black = no change (1:1 ratio) Or Green = control condition (e.g. aerobic) Red = experimental condition (e.g. anaerobic) We only use ratio Campbell & Heyer, 2003
Clustering of example Campbell & Heyer, 2003
Clustering of entire yeast genome Campbell & Heyer, 2003
SMD Database
Microarray software
Microarray databases and tools
Microarray tools NetAffix Analysis center from affymetrix Array content information Probe sequences Gene annotations Xcluster- tool for cluster analysis GENECLUSTER TIGR Microarray MADAM- Microarray data manager SPOTFINDER -image processing tool MIDAS -Microarray data analysis system MEV -MultiExperiment Viewer
ARRAY EXPRESS (EBI)
GEO(NCBI)

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Microarray

  • 1. DNA Microarrays Ms.ruchi yadav lecturer amity institute of biotechnology amity university lucknow(up)
  • 2. Gene expression A human organism has over 250 different cell types (e.g., muscle, skin, bone, neuron), most of which have identical genomes, yet they look different and do different jobs It is believed that less than 20% of the genes are‘expressed’ (i.e., making RNA) in a typical cell type Apparently the differences in gene expression is what makes the cells different
  • 8. Microarrays: Universal Biochemistry Platforms Peptides Proteins Carbohydrates Lipids Small molecules DNA
  • 9. Some questions for the golden age of genomics How gene expression differs in different cell types? How gene expression differs in a normal and diseased (e.g., cancerous) cell? How gene expression changes when a cell is treated by a drug? How gene expression changes when the organism develops and cells are differentiating? How gene expression is regulated – which genes regulate which and how?
  • 10. What is a DNA Microarray? (cont.) Biological Samples in 2D Arrays on Membranes or Glass Slides Cheung et al. 1999
  • 11. What is a DNA Microarray? Also known as DNA Chip Allows simultaneous measurement of the level of transcription for every gene in a genome (gene expression) Microarray detects mRNA, or rather the more stable cDNA
  • 13. The Colours of a Microarray GREEN represents Control DNA , where either DNA or cDNA derived from normal tissue is hybridized to the target DNA. RED represents Sample DNA , where either DNA or cDNA is derived from diseased tissue hybridized to the target DNA. YELLOW represents a combination of Control and Sample DNA , where both hybridized equally to the target DNA. BLACK represents areas where neither the Control nor Sample DNA hybridized to the target DNA.
  • 14. Microarray Steps Experiment and Data Acquisition Sample preparation and labelling Hybridisation Washing Image acquisition Data normalization Data analysis Biological interpretation
  • 15. I. Target and probe preparation
  • 16. There are many ways to obtain a labeled target sample. ...GGCUUAAUGAGCCUUAAAAAA...A mRNA TTTTTT...T viral enzyme reverse transcriptase recognizes poly-T bound to poly-A and begins to add complementary DNA nucleotides. The C nucleotides are dyed. A A A G G C T C T T A A G C C ... poly-A tail cDNA target poly-T primer
  • 20. How do we manufacture a microarray? Start with individual genes, e.g. the ~6,200 genes of the yeast genome Amplify all of them using polymerase chain reaction (PCR) “ Spot” them on a medium, e.g. an ordinary glass microscope slide Each spot is about 100 µm in diameter Spotting is done by a robot Complex and potentially expensive task
  • 23. DNA Samples on 96 well plates
  • 24. The PixSys 5500 Arraying Robot (Cartesian Technologies) Vacuum wash station The print head holds up to 32 pins in a 8x4 format Vacuum hold-down platform (50 slide capacity) Robotic arm
  • 26. Non Contact Printing InkJet (HP/Canon) technology • 1 drop = 100 picolitres
  • 28. Spotting the Probes on the Microarray 8 X 4 Print Head microarray slide plate with wells holding probes in solution All spots of the same color are made at the same time. All spots in the same sector are made by the same pin.
  • 29. Using cDNA Microarrays to Measure mRNA Levels ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? Sample 1 Sample 2 Microarray Slide Spots (Probes) Unknown mRNA Sequences (Target)
  • 30. Extract mRNA ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
  • 31. Convert to cDNA and Label with Fluorescent Dyes ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
  • 32. Mix Labeled cDNA ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
  • 33. Hybridize cDNA to the Slide ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????
  • 34. Excite Dyes with Laser Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G
  • 35. Scan Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G
  • 36. Quantify Signals ACCTG...G 7652 138 TTCTG...A 5708 4388 GGCTT...C 8566 765 ATCTA...A 1208 13442 ACGGG...T 6784 9762 CGATA...G 67 239 Sample 1 Sample 2
  • 40. Oligonucleotide Microarray Gene chip (DNA chip, Affymetrix chip): Oligonucleotide (20~80-mer oligos) is synthesized either in situ (on-chip) Developed at Affymetrix, Inc. , under the GeneChip® trademark
  • 41. Affymetrix Chip Each gene has 16 – 20 pairs of probes synthesized on the chip Each pairs of probes have two oligonucleotide – Perfect match (PM, reference seq) ATG…C…TGC (20-25 bases) – Mismatch (MM, one base change) ATG… T …TGC A MM oligo is identical to a PM oligo except that the middle nucleotide (13 th of 25) is intentionally replaced by its complementary nucleotide . The scanned result for a given gene is the average differences between PM and MM signals, over probes
  • 42. Different Probe Pairs Represent Different Parts of the Same Gene gene sequence Probes are selected to be specific to the target gene and have good hybridization characteristics.
  • 43. A Probe Set for Measuring Expression Level of a Particular Gene probe pair gene sequence ...TGCAATGGGTCAGAA G GACTCCTATGTGCCT... AATGGGTCAGAA G GACTCCTATGTG AATGGGTCAGAA C GACTCCTATGTG perfect match sequence mismatch sequence probe set probe cell
  • 45. The photolithographic method Treat substrate with chemically protected “linker” molecules, creating rectangular array Selectively expose array sites to light deprotects exposed molecules, activating further synthesis Flush chip surface with solution of protected A,C,G,T Binding occurs at previously deprotected sites Repeat steps 2&3 until desired probes are synthesized
  • 46. Photolithography The mask only allows light to pass to specific features on the chip
  • 48. Affymetrix chip Photolithographic Approach In-situ synthesis of oligonucleotide
  • 51. Affymetrix GeneChips The black features represent no intensity (no RNA hybridized to the respective probe in the feature). The intensity level from lowest to highest by color is: Dark blue -> Blue -> Light Blue -> Green -> Yellow -> Orange -> Red - > White . More intensity means more RNA bound to a specific feature, which basically means the gene was expressed at a higher level.
  • 53. Affymetrix GeneChip experiment labeled cRNA randomly fragmented in to pieces anywhere from 30 to 400 base pairs in length The fragmented, Biotin-labeled cRNA is added to the array Anywhere on the array where a RNA fragment and a probe are complimentary, the RNA hybridizes to the probes in the feature. The array is then washed to remove any RNA that is not stuck to an array then stained with the fluorescent molecule that sticks to Biotin (Cy5 conjugated to streptavidin) Lastly, the entire array is scanned with a laser and the information is kept in a computer for quantitative analysis of what genes were expressed and at what approximate level
  • 54. in-situ synthesised arrays The different methods for deprotection lead to the three main technologies for making in-situ synthesised arrays: Photodeprotection using masks: this is the basis of the Affymetrix® technology. Photodeprotection without masks : this is the method used by Nimblegen and Febit. Chemical deprotection with synthesis via inkjet technology: this is the method used by Rosetta, Agilent and Oxford Gene Technology.
  • 60. * Measuring levels of gene expression * Creating diagnostic tests to predict whether a patient has a genetic predisposition to obesity * Designing Drugs Gene expression and obesity
  • 61. Reading an array (cont.) Campbell & Heyer, 2003 Block Column Row Gene Name Red Green Red:Green Ratio 1 1 1 tub1 2,345 2,467 0.95 1 1 2 tub2 3,589 2,158 1.66 1 1 3 sec1 4,109 1,469 2.80 1 1 4 sec2 1,500 3,589 0.42 1 1 5 sec3 1,246 1,258 0.99 1 1 6 act1 1,937 2,104 0.92 1 1 7 act2 2,561 1,562 1.64 1 1 8 fus1 2,962 3,012 0.98 1 1 9 idp2 3,585 1,209 2.97 1 1 10 idp1 2,796 1,005 2.78 1 1 11 idh1 2,170 4,245 0.51 1 1 12 idh2 1,896 2,996 0.63 1 1 13 erd1 1,023 3,354 0.31 1 1 14 erd2 1,698 2,896 0.59
  • 62. Color Coding Tables are difficult to read Data is presented with a color scale Coding scheme: Green = repressed (less mRNA) gene in experiment Red = induced (more mRNA) gene in experiment Black = no change (1:1 ratio) Or Green = control condition (e.g. aerobic) Red = experimental condition (e.g. anaerobic) We only use ratio Campbell & Heyer, 2003
  • 63. Clustering of example Campbell & Heyer, 2003
  • 64. Clustering of entire yeast genome Campbell & Heyer, 2003
  • 68. Microarray tools NetAffix Analysis center from affymetrix Array content information Probe sequences Gene annotations Xcluster- tool for cluster analysis GENECLUSTER TIGR Microarray MADAM- Microarray data manager SPOTFINDER -image processing tool MIDAS -Microarray data analysis system MEV -MultiExperiment Viewer