DNA Microarrays Databases and Statistics 1st

Edition Alan R. Kimmel pdf download

[Link]

★★★★★ 4.7/5.0 (33 reviews) ✓ 205 downloads ■ TOP RATED

"Excellent quality PDF, exactly what I needed!" - Sarah M.

DOWNLOAD EBOOK
 DNA Microarrays Databases and Statistics 1st Edition Alan R.
Kimmel pdf download

TEXTBOOK EBOOK EBOOK GATE

Available Formats

■ PDF eBook Study Guide TextBook

EXCLUSIVE 2025 EDUCATIONAL COLLECTION - LIMITED TIME

INSTANT DOWNLOAD VIEW LIBRARY

Instant digital products (PDF, ePub, MOBI) available
Download now and explore formats that suit you...

Cancer Diagnostics with DNA Microarrays 1st Edition Steen

Knudsen

[Link]
microarrays-1st-edition-steen-knudsen/

[Link]

DNA Microarrays and Gene Expression From Experiments to

Data Analysis and Modeling 1st Edition Pierre Baldi

[Link]
from-experiments-to-data-analysis-and-modeling-1st-edition-pierre-
baldi/
[Link]

Nutrition and Sensation 1st Edition Alan R. Hirsch

[Link]
alan-r-hirsch/

[Link]

Statistics for Censored Environmental Data Using Minitab

and R Statistics in Practice 2nd Edition Dennis R. Helsel

[Link]
data-using-minitab-and-r-statistics-in-practice-2nd-edition-dennis-r-
helsel/
[Link]
Probability and Statistics with R 1st Edition Maria
Dolores Ugarte

[Link]
edition-maria-dolores-ugarte/

[Link]

Advanced C Programming 1st Edition Paul Kimmel

[Link]
kimmel/

[Link]

New High Throughput Technologies for DNA Sequencing and

Genomics 1st Edition Keith R. Mitchelson (Eds.)

[Link]
dna-sequencing-and-genomics-1st-edition-keith-r-mitchelson-eds/

[Link]

Statistics Explained 3rd Edition Perry R. Hinton

[Link]
r-hinton/

[Link]

Peptide Microarrays Methods and Protocols 1st Edition

Victor E. Tapia

[Link]
protocols-1st-edition-victor-e-tapia/

[Link]
METHODS IN ENZYMOLOGY
EDITORS-IN-CHIEF

John N. Abelson Melvin I. Simon

DIVISION OF BIOLOGY
CALIFORNIA INSTITUTE OF TECHNOLOGY
PASADENA, CALIFORNIA

FOUNDING EDITORS

Sidney P. Colowick and Nathan O. Kaplan

 Table of Contents

CONTRIBUTORS TO VOLUME 410 . . . . . . . . . . . . . . . . . ix

VOLUMES IN SERIES . . . . . . . . . . . . . . . . . . . . . xiii

Section I. Array Platforms

1. The Affymetrix GeneChipÒ Platform: DENNISE D.
An Overview DALMA-WEISZHAUSZ,
JANET WARRINGTON,
EUGENE Y. TANIMOTO, AND
C. GARRETT MIYADA 3

2. The Agilent In Situ-Synthesized PAUL K. WOLBER,

Microarray Platform PATRICK J. COLLINS,
ANNE B. LUCAS,
ANNIEK DE WITTE, AND
KAREN W. SHANNON 28
3. Illumina Universal Bead Arrays JIAN-BING FAN,
KEVIN L. GUNDERSON,
MARINA BIBIKOVA,
JOANNE M. YEAKLEY,
JING CHEN,
ELIZA WICKHAM GARCIA,
LORI L. LEBRUSKA,
MARC LAURENT,
RICHARD SHEN, AND
DAVID BARKER 57

4. Microarray Oligonucleotide Probes DAVID P. KREIL,

ROSLIN R. RUSSELL, AND
STEVEN RUSSELL 73

5. Automated Liquid Handling and High- ANGELA BURR,

Throughput Preparation of Polymerase KEVIN BOGART,
Chain Reaction-Amplified DNA for JASON CONATY, AND
Microarray Fabrication JUSTEN ANDREWS 99
6. The Printing Process: Tips on Tips REED A. GEORGE 121
7. Making and Using Spotted DNA Microarrays JANET HAGER 135
in an Academic Core Laboratory

v
vi table of contents

8. Printing Your Own Inkjet Microarrays CHRISTOPHER G. LAUSTED,

CHARLES B. WARREN,
LEROY E. HOOD, AND
STEPHEN R. LASKY 168
9. Peptide Nucleic Acid Microarrays Made with MARK A. WITSCHI,
(S,S)-trans-Cyclopentane-Constrained JONATHAN K. POKORSKI, AND
Peptide Nucleic Acids DANIEL H. APPELLA 189

Section II. Wet-Bench Protocols

10. Optimizing Experiment and Analysis SCOTT J. NEAL AND
Parameters for Spotted Microarrays J. TIMOTHY WESTWOOD 203
11. Sample Labeling: An Overview MICHAEL BROWNSTEIN 222

12. Genomic DNA as a General Cohybridization BRIAN A. WILLIAMS,

Standard for Ratiometric Microarrays RICHELE M. GWIRTZ, AND
BARBARA J. WOLD 237

13. Analysis of Sequence Specificities of MARTHA L. BULYK 279

DNA-Binding Proteins with
Protein Binding Microarrays

14. Microarray Analysis of RNA Processing TIMOTHY R. HUGHES,

and Modification SHAWNA L. HILEY,
ARNEET L. SALTZMAN,
TOMAS BABAK, AND
BENJAMIN J. BLENCOWE 300

15. Mapping the Distribution of Chromatin NICOLAS NÈGRE,

Proteins by ChIP on Chip SERGEY LAVROV,
JÉRÔME HENNETIN,
MICHEL BELLIS, AND
GIACOMO CAVALLI 316
16. DamID: Mapping of In Vivo Protein–Genome FRAUKE GREIL,
Interactions Using Tethered DNA Adenine CELINE MOORMAN, AND
Methyltransferase BAS VAN STEENSEL 342
 table of contents vii

17. Whole-Genome Genotyping KEVIN L. GUNDERSON,

FRANK J. STEEMERS,
HONGI REN, PAULINE NG,
LIXIN ZHOU, CHAN TSAN,
WEIHUA CHANG, DAVE BULLIS,
JOE MUSMACKER,
CHRISTINE KING,
LORI L. LEBRUSKA,
DAVID BARKER,
ARNOLD OLIPHANT,
KENNETH M. KUHN, AND
RICHARD SHEN 359
18. Mapping Drosophila Genomic Aberration JEREMY N. ERICKSON AND
Breakpoints with Comparative Genome ERIC P. SPANA 377
Hybridization on Microarrays

19. Performing Quantitative Reverse-Transcribed GEORGES LUTFALLA AND

Polymerase Chain Reaction Experiments GILLES UZE 386
20. The Application of Tissue Microarrays in the STEPHEN M. HEWITT 400
Validation of Microarray Results

21. Mapping Histone Modifications by DAVID J. CLARK AND

Nucleosome Immunoprecipitation CHANG-HUI SHEN 416

AUTHOR INDEX . . . . . . . . . . . . . . . . . . . . . . 431

SUBJECT INDEX . . . . . . . . . . . . . . . . . . . . . . 461
 Contributors to Volume 410
Article numbers are in parentheses and following the name of contributors.
Affiliations listed are current.

JUSTEN ANDREWS (5), Department of MARTHA L. BULYK (13), Division of

Biology, Drosophila Genomics Resource Genetics, Departments of Medicine and
Center, Center for Genomics and Bioin- Pathology, Harvard-MIT Division of
formatics, Indiana University, Blooming- Health Sciences & Technology (HST),
ton, Indiana Brigham & Women’s Hospital, Harvard
Medical School, Boston, Massachusetts
DANIEL H. APPELLA (9), Laboratory of
Bioorganic Chemistry, NIDDK, NIH, ANGELA BURR (5), Drosophila Genomics
DHHS Bethesda, Maryland and Resource Center, Center for Genomics
Department of Chemistry, Northwestern and Bioinformatics, Indiana University,
University, Evanston, Illinois Bloomington, Indiana
TOMAS BABAK (14), Banting and Best GIACOMO CAVALLI (15), Chromatin and
Department of Medical Research, Cell Biology Lab, Institute of Human
Department of Medical and Molecular Genetics – CNRS, Montpellier, Cedex 05,
Genetics, University of Toronto, Toronto, France
Ontario, Canada
WEIHUA CHANG (17), Illumina, Inc., San
DAVID BARKER (3, 17), Illumina, Inc., San Diego, California
Diego, California
JING CHEN (3), Illumina, Inc., San Diego,
MICHEL BELLIS (15), Centre de Recherche California
en Biochimie Macromoleculaire,
Montpellier, Cedex 05, France DAVID J. CLARK (21), Laboratory of Mole-
cular Growth Regulation, NICHD,
MARINA BIBIKOVA (3), Illumina, Inc., San National Institutes of Health, Bethesda,
Diego, California Maryland
BENJAMIN J. BLENCOWE (14), Banting and PATRICK J. COLLINS (2), Microarray Qual-
Best Department of Medical Research, ity Agilent Technologies, Inc., Santa
Department of Medical and Molecular Clara, California
Genetics, Microbiology, University of
Toronto, Toronto, Ontario, Canada JASON CONATY (5), Drosophila Genomics
Resource Center, Center for Genomics
KEVIN BOGART (5), Drosophila Genomics and Bioinformatics, Indiana University,
Resource Center, Center for Genomics Bloomington, Indiana
and Bioinformatics, Indiana University,
Bloomington, Indiana DENNISE D. DALMA-WEISZHAUSZ (1), Ex-
pression Product Development, AFFY-
MICHAEL BROWNSTEIN (11), The J. Craig METRIX, INC., Santa Clara, California
Venter Institute, Rockville, Maryland
ANNIEK DE WITTE (2), Microarray Quality
DAVE BULLIS (17), Illumina, Inc., San Agilent Technologies, Inc., Santa Clara,
Diego, California California

ix
x CONTRIBUTORS TO VOLUME 410

JEREMY N. ERICKSON (18), Model System DAVID P. KREIL (4), Department of

Genomics, Department of Biology, Duke Biotechnology, University of Natural
University, Durham, North Carolina Resources and Applied Life Sciences,
Vienna, Austria
JIAN-BING FAN (3), Illumina, Inc., San
Diego, California KENNETH M. KUHN (17), Illumina, Inc.,
San Diego, California
ELIZA WICKHAM GARCIA (3), Illumina,
Inc., San Diego, California STEPHEN R. LASKY (8), Institute for Systems
Biology, Seattle, Washington
REED A. GEORGE (6), Howard Hughes
Medical Institute, Janelia Farm Research MARC LAURENT (3), Illumina, Inc., San
Campus, Ashburn, Virginia Diego, California
FRAUKE GREIL (16), Division of Molecular CHRISTOPHER G. LAUSTED (8), Institute for
Biology, Netherlands Cancer Institute, Systems Biology, Seattle, Washington
Amsterdam, The Netherlands
SERGEY LAVROV (15), Chromatin and Cell
KEVIN L. GUNDERSON (3, 17), Illumina,
Biology Lab, Institute of Human
Inc., San Diego, California
Genetics – CNRS, Montpellier, Cedex
RICHELE M. GWIRTZ (12), Biology Division 05, France
156-29, Caltech, Pasadena, California
LORI L. LEBRUSKA (3, 17), Illumina, Inc.,
JANET HAGER (7), W.M. Keck Biotechnology San Diego, California
Resource Laboratory, Yale University,
New Haven, Connecticut ANNE B. LUCAS (2), Microarray Quality
Agilent Technologies, Inc., Santa Clara,
JÉRÔME HENNETIN (15), Centre de Recherche California
en Biochimie Macromoleculaire, Montpel-
lier, Cedex 05, France GEORGES LUTFALLA (19), UMR5124, cc86
CNRS/Université Montpellier II,
STEPHEN M. HEWITT (20), Tissue Array Montpellier, Cedex 05, France
Research Program, Laboratory of Pathol-
ogy, CCR, NCI, NIH TARP Lab, C. GARRETT MIYADA (1), Expression
Advanced Technology Center, Bethesda, Product Development, AFFYMETRIX,
Maryland INC., Santa Clara, California

SHAWNA L. HILEY (14), Banting and Best CELINE MOORMAN (16), Division of
Department of Medical Research, Uni- Molecular Biology, Netherlands Cancer
versity of Toronto, Toronto, Ontario, Institute, Amsterdam, The Netherlands
Canada
JOE MUSMACKER (17), Illumina, Inc., San
LEROY E. HOOD (8), Institute for Systems Diego, California
Biology, Seattle, Washington
SCOTT J. NEAL (10), Department of
TIMOTHY R. HUGHES (14), Banting and Zoology, University of Toronto, Cana-
Best Department of Medical Research, dian Drosophila Microarray Centre,
Department of Medical and Molecular Mississauga, Ontario, Canada
Genetics, University of Toronto, Toronto,
Ontario, Canada NICOLAS NÈGRE (15), Chromatin and
Cell Biology Lab, Institute of Human
CHRISTINE KING (17), Illumina, Inc., San Genetics – CNRS, Montpellier, Cedex 05,
Diego, California France
 CONTRIBUTORS TO VOLUME 410 xi

PAULINE NG (17), Illumina, Inc., San Diego, EUGENE Y. TANIMOTO (1), Expression
California Product Development, AFFYMETRIX,
INC., Santa Clara, California
ARNOLD OLIPHANT (17), Illumina, Inc., San
Diego, California CHAN TSAN (17), Illumina, Inc., San Diego,
California
JONATHAN K. POKORSKI (9), Laboratory
of Bioorganic Chemistry, NIDDK, GILLES UZE (19), UMR5124, cc86 CNRS/
NIH, DHHS Bethesda, Maryland and Université Montpellier II, Cedex 05,
Department of Chemistry, Northwestern France
University, Evanston, Illinois
BAS VAN STEENSEL (16), Division of
HONGI REN (17), Illumina, Inc., San Diego, Molecular Biology, Netherlands Cancer
California Institute, Amsterdam, The Netherlands

ROSLIN R. RUSSELL (4), Department of CHARLES B. WARREN (8), Institute for

Genetics, University of Cambridge, Systems Biology, Seattle, Washington
Cambridge, United Kingdom
JANET WARRINGTON (1), Expression
STEVEN RUSSELL (4), Department of Product Development, AFFYMETRIX,
Genetics, University of Cambridge, INC., Santa Clara, California
Cambridge, United Kingdom
J. TIMOTHY WESTWOOD (10), Department
ARNEET L. SALTZMAN (14), Banting and of Zoology, University of Toronto,
Best Department of Medical Research, Canadian Drosophila Microarray
Department of Medical and Molecular Centre, Mississauga, Ontario, Canada
Genetics, Microbiology, University of BRIAN A. WILLIAMS (12), Biology Division
Toronto, Toronto, Ontario, Canada 156-29, Caltech, Pasadena, California
KAREN W. SHANNON (2), Microarray MARK A. WITSCHI (9), Laboratory of
Quality Agilent Technologies, Inc., Bioorganic Chemistry, NIDDK, NIH,
Santa Clara, California DHHS Bethesda, Maryland and Depart-
ment of Chemistry, Northwestern
CHANG-HUI SHEN (21), Institute for Macro- University, Evanston, Illinois
molecular Assemblies, CUNY, Depart-
ment of Biology, College of Staten PAUL K. WOLBER (2), Microarray Quality
Island, Staten Island, New York Agilent Technologies, Inc., Santa Clara,
California
RICHARD SHEN (3, 17), Illumina, Inc., San
Diego, California BARBARA J. WOLD (12), Biology Division
156-29, Caltech, Pasadena, California
ERIC P. SPANA (18), Model System
Genomics, Department of Biology, Duke JOANNE M. YEAKLEY (3), Illumina, Inc.,
University, Durham, North Carolina San Diego, California

FRANK J. STEEMERS (17), Illumina, Inc., LIXIN ZHOU (17), Illumina, Inc., San
San Diego, California Diego, California
[1] the affymetrix genechip platform 3

[1] The Affymetrix GeneChipÒ Platform: An Overview

By DENNISE D. DALMA‐WEISZHAUSZ, JANET WARRINGTON,
EUGENE Y. TANIMOTO , and C. GARRETT MIYADA

Abstract
The intent of this chapter is to provide the reader with a review of
GeneChip technology and the complete system it represents, including its
versatility, components, and the exciting applications that are enabled by
this platform. The following aspects of the technology are reviewed: array
design and manufacturing, target preparation, instrumentation, data analy-
sis, and both current and future applications. There are key differentiators
between Affymetrix’ GeneChip technology and other microarray‐based
methods. The most distinguishing feature of GeneChip microarrays is that
their manufacture is directed by photochemical synthesis. Because of this
manufacturing technology, more than a million different probes can be
synthesized on an array roughly the size of a thumbnail. These numbers
allow the inclusion of multiple probes to interrogate the same target
sequence, providing statistical rigor to data interpretation. Over the years
the GeneChip platform has proven to be a reliable and robust system,
enabling many new discoveries and breakthroughs to be made by the
scientific community.

Introduction
Starting in the 1990s, a genomic revolution, propelled by major techno-
logical advances, has enabled scientists to complete the sequences of a
variety of organisms, including viruses, bacteria, invertebrates, and culmi-
nating in the full draft sequence of the human genome (Lander et al., 2001).
In the wake of this flood of sequence information, scientists are currently
faced with the daunting task of translating genomic sequence information
into functional biological mechanisms that will allow a better understand-
ing of life and its disease states and hopefully offer better diagnostics and
novel therapeutic interventions. High‐density microarrays are uniquely
qualified to tackle this daunting task and have therefore become an essen-
tial tool in life sciences research. They provide a reliable, fast, and cost‐
effective method that effectively scales with the ever‐increasing amounts of
genomic information.

METHODS IN ENZYMOLOGY, VOL. 410 0076-6879/06 $35.00

Copyright 2006, Elsevier Inc. All rights reserved. DOI: 10.1016/S0076-6879(06)10001-4
4 array platforms [1]

In the last decade, there has been an immense growth in the use of high‐
throughput microarray technology for three major genetic explorations:
the genome‐wide analysis of gene expression, SNP genotyping, and rese-
quencing. While many of these studies have focused on human subjects and
diseases, microarrays are also being used to study the gene expression and
sequence variation of a variety of model organisms, such as yeast,
Drosophila, mice, and rats. New applications are rapidly emerging, such
as the discovery of novel transcripts (from coding and noncoding regions),
the identification of novel regulatory sequences, and the characterization
of functional domains in the RNA transcript. Integrating all of the infor-
mation emanating from whole‐genome studies will undoubtedly allow a
more global understanding of the genome and the regulatory circuits that
govern its activity.
The comparison of genome‐wide expression patterns provides research-
ers with an objective and hypothesis‐free method to better understand
the dynamic relationship between mRNA content and biological function.
This method has enabled scientists to discover, for example, the genetic
pathways that are changed and disrupted in a wide range of diseases,
from cancer (Armstrong et al., 2002; Huang et al., 2004; Yeoh et al., 2002)
to multiple sclerosis (Steinman and Zamvil, 2003). Across multiple disci-
plines, whole‐genome expression analysis is helping scientists to stratify
disease states, predict patient outcome, and make better therapeutic
choices. Some of the recent examples of scientific and medical findings
utilizing this technology include the identification of murine longevity genes
and the discovery of novel transcripts that question our basic understanding
of gene expression (Kapranov et al., 2002).
The most recent generation of GeneChip microarrays for DNA
sequence analysis allows scientists to genotype single nucleotide poly-
morphisms on a genome‐wide scale (Kennedy et al., 2003; Matsuzaki
et al., 2004a,b). The ability to quickly genotype over 100,000 single
nucleotide polymorphisms (SNPs) distributed across the human genome
has allowed researchers to conduct linkage analysis and genetic associa-
tion studies. These new tools for disease mapping studies have already
helped scientists pinpoint genes linked to diseases such as sudden infant
death syndrome (Puffenberger et al., 2004), neonatal diabetes (Sellick
et al., 2003), and bipolar disorder (Middleton et al., 2004). The technology
has proven to be scalable, and assays that cover 500,000 SNPs are now
available.
Microarrays have revolutionized basic scientific research and are con-
stantly challenging our view of the genome and its complexity. They are
finding their way from the research laboratory to the clinic, where they
promise the same kind of revolution in patient care. Microarrays used in
[1] the affymetrix genechip platform 5

clinical research and clinical applications promise to help scientists develop

more accurate diagnostics and create novel therapeutics. By standardizing
microarray data and integrating it with a patient’s existing medical records,
physicians can offer more tailored and more successful therapies. The
combination of a patient’s genetic and clinical data will allow for person-
alized medicine, which is where GeneChip technology holds the greatest
promise to improve health.

GeneChip Microarrays, a Flexible Platform

GeneChip arrays are the result of the combination of a number of
technologies, design criteria, and quality control processes. In addition to
the arrays, the technology relies on standardized assays and reagents,
instrumentation (fluidics system, hybridization oven and scanner), and data
analysis tools that have been developed as a single platform. The key assay
steps are outlined in Fig. 1 and are discussed in greater detail in later
sections along with array design and manufacturing. The considerable
flexibility of the GeneChip system and the manufacturing technology
allows the design of the arrays to be dictated by their intended use, such
as whole‐genome transcriptome mapping, gene expression profiling, or
custom genotyping. In addition to GeneChip catalogue microarrays (over
50 arrays and array sets are currently available), a custom program exists,
where researchers can design their own arrays for organisms not covered
by existing products and for specialized or directed studies. These designs
may be based on many of the same design features and manufacturing
techniques available in catalogue arrays (probe selection algorithms,
manufacturing control tests, etc.) and are expected to provide customers
equivalent performance to their commercial counterparts.

Array Manufacturing
Adapting technologies used in the semiconductor industry, GeneChip
array manufacturing begins with a 5‐in.2 quartz wafer (Fodor et al., 1991;
McGall and Christians, 2002). This substrate is first modified covalently
with a silane reagent to produce a stable surface layer of hydroxyalkyl
groups. Linker molecules with photolabile‐protecting groups are then at-
tached covalently to this layer to create a surface that may be spatially
activated by light (Fig. 2). A photolithographic mask set that represents the
sequence information content on the array is carefully designed. Each
mask is manufactured with windows that either block or permit the trans-
mission of ultraviolet light. These windows are distributed over the mask
based on the desired sequence of each probe. The mask is carefully aligned
6 array platforms [1]

FIG. 1. Flowchart of a GeneChip System microarray experiment. Once the nucleic acid
sample has been obtained, target amplification and labeling result in a labeled sample. The
labeled sample is then injected into the probe array and allowed to hybridize overnight in the
hybridization oven. Probe array washing and staining occur on the fluidics station, which can
handle four probe arrays simultaneously. The probe array is then ready to be scanned in the
Affymetrix GeneChip scanner, where the fluorescence intensity of each feature is read. Data
output includes an intensity measurement for each transcript or the detailed sequence or
genotyping (SNP) information.

with the quartz wafer, which ensures that oligonucleotide synthesis is only
activated at precise locations on the wafer. When near‐ultraviolet light
shines through the mask, terminal hydroxyl groups on the linker molecules
in exposed areas of the wafer are deprotected, thereby activating them for
nucleotide coupling, while linkers in unexposed regions remain protected
and inactive. A solution containing a deoxynucleoside phosphoramidite
monomer with a light‐sensitive protecting group is flushed over the surface
of the wafer, and the nucleoside attaches to the activated linkers (coupling
step), initiating the synthesis process.
Oligonucleotide synthesis proceeds by repeating the two basic steps:
deprotection and coupling. For each round of synthesis, deprotection gen-
erally uses a unique mask from the designed set. The coupling steps
alternate through the addition of A‐, C‐, G‐, or T‐modified nucleotides.
The deprotection and coupling cycle is repeated until all of the full‐length
probe sequences, usually 25‐mers, are completed. Algorithms that optimize
[1] the affymetrix genechip platform 7

FIG. 2. Manufacture of a GeneChip probe array. (A) Photolithography. (Left) Near‐

ultraviolet light is passed through a mask containing open windows. The size and the location
of each open window delineate the surface on the quartz wafer that will be activated for
chemical synthesis. The use of sequential masks in conjunction with the chemical synthesis
creates a cycle that directs the precise sequence synthesis of oligonucleotides that compose the
array. (Right) The photolithographic process. (B) (Left) Schematic representation of the
nucleic acid synthesis cycle. Light removes protecting groups (squares) at defined areas on
the array. A single nucleotide is washed over the array and couples to the deprotected areas.
Through successive steps, any oligonucleotide sequence can be built on each feature of the
array. The number of steps required to build a 25 nucleotide sequence on the array is 100,
although the optimization of mask usage has lowered that number to
75 steps. (Right) The
chemical synthesis station, where nucleotide binding occurs. (C) (Left) Complete synthesis on
8 array platforms [1]

mask usage allow the creation of the arrays in significantly fewer than
the 100 cycles that would normally be required to synthesize all possible
25‐mer sequences (Lipshutz et al., 1995). The information density of the
array depends on the spatial resolution of the photolithographic process.
Once oligonucleotide synthesis is complete, wafers can be diced in a
variety of array sizes and packaged individually into cartridges. Generally,
each 5‐in. square wafer can yield between 49 and 400 identical GeneChip
microarrays, depending on the amount of genetic information required.
A typical 1.28‐cm2 array (49‐format), for example, will contain more than
1.4 million different probe locations, or features, assuming the features are
spaced 11 m apart. Each of these features contains millions of identical
DNA molecules. A reduction of the feature spacing to 5 m (as available
on the Mapping 500K Array Set released in September of 2005) produces
over 6.5 million different features on the same 1.28‐cm2 array—an expo-
nential increase in the available data from a single experiment. This dem-
onstrates the power of ‘‘feature shrink’’ on the Affymetrix microarray
platform. The manufacturing process ends with a comprehensive series of
quality control tests to ensure that GeneChip arrays deliver accurate and
reproducible data.

Array Design
Array design is closely coupled to sample preparation and the
biological question to be addressed. Specific examples are described in
greater detail for expression and genotyping applications. Almost all of
the designs utilize two types of probes: (1) probes that have complete
complementarity to their target sequence [perfect match probe (PM)]
and (2) probes with a single mismatch to the target, centered in the middle
of the oligonucleotide [mismatch probe (MM), Fig. 3]. The number of
probes used to interrogate a specific SNP or transcript is selected to meet
specific performance criteria for each assay.
In addition to the probes specific for a particular assay, arrays contain
a number of different control probes. There are probes specific for qual-
ity control assays. Another set of probes is arranged in checkerboard
patterns on the array. These probes bind to a specific biotinylated oligonu-
cleotide included in the hybridization cocktail. Following scanning, these

the wafer results in many (49–400) identical high‐density oligonucleotide microarrays in one
wafer. Dicing of the wafer into individual microarrays occurs, and each microarray is inserted
into a plastic cartridge. (Right) Machinery used to incorporate the diced microarray into the
plastic cartridge.
danger of that

among

is

Straits E pain

swing it

the AN
bacon the

India when

to

Sea in

was photographs It

ground FROM almost

terrier in deer

Mole skunks

grizzly sort torn

The permission possession

instruments dead Australia

which appearance

peasants

A seldom
following on

the are are

the

the best

S Z where

the

search A a

is cities

us difficult highly

collection
RAT

Sons the

the

possibly it

to are

for

distance taken except

warn
the

in

worst

true used

distinction and the

that by the

for where

fine and

Africa Oryx The

12
cold

pretended

this was

which s

a small elephant

failed was

a but was

of view Old

INSANGS grass
domestic chimpanzee

a wished she

fields 290

waited examples

stands exquisite

OF
at in to

of 210

in

Berlin HINCHILLA

doubt

is the natives

Solway The would

curve
apparently

pageants the as

a pages kills

in having EMUR

distance marked
as

bitten

are

of

with and

developed great of

the

exquisite these It

more some

a houses
on the

is gives tailed

of

claws

of

and

extended these
is between a

one

is cold

driven huts

the

India fortunately

fruit

mining Short showmen

theory compared

It of
but

die and

and in the

for

as shades

a hand crown

Baker soko under

feline
been

some

grow

Anschütz

with Boers

had a of
Editor states chestnuts

a like

with

looked

large

bones which killed

different Small persons

as snow of

males saw wolves

all

This it

men This M

sent

spines

and up Madagascar
light his

that on coats

mauled

The a assembles

The II
even one of

ways Clew

at species equal

On an four

log of

This pig
armed tinge

by tusks the

numbers hair the

mouth I larger

upon by

Mole water home

them

of W

and Duchess
of are urus

confined resource

the different

small he measured

means

the both any

he

ordinary
rear others

lower

the tree

Some of of

am growls believed

to is

The high sensations

laughed the

hoofs
seaweed in trees

has the is

Dallas and of

great and Photo

that been

his The
and We than

single estuaries capital

maturity very ground

stallions

bull 59 molest
American

as are A

of that

of yellow

like

from Sons It

Romans dry CUB

his fish

2 we or

deserve

in in

some

and to

days Sowerby travel

the them Kalahari

the which S
busily then

for is squirrels

a are

it is

of holes

INSECTS flattened

known Swamp come

Baker brown destroy

cat
A of

in of

line in

the any would

Adventures menageries

have

body attack
the to that

have and

stories made dealing

COMMON furnished

medicine Chaillu the

side
H colour fact

and from of

staves the

they

full him generations

the tint

restricted her

and or HE

eagerly by

in
called

and a the

tail

making few continual

of

years the of

Later packs same

or an CAT

very
Reid

struck severely the

with terriers

in
within

Sydney to

British dominated till

alone MONKEY seals

the rushed
found and

shoot sharp a

lines of

are

for the

he than the

it seen

OLE on sit

Egypt and

sized
though any

very Medland

following

sea

by

with a

palm

the and

the

to Photo in
lemmings

cat THE than

201 Croydon sounds

by The except

Land attached Another

of

in

exceedingly

another

use whilst gathering

for is

AUSTRALIAN

naturalists and the

the these were

skulls

will

death a

the and

the

at about
best driven

the

it are unless

coyotes the of

the on

savagely
well

dog great century

and most while

we the its

family left

Norway is three
draw bulls

who

plains able spirit

turn endeavour

shot rescue

was fore
down this any

Epping

like of

struck

cornered

at

the that
of

four hear a

Englishman

and grubs

rodents forwards
a many

usually and

ENRECS is grass

the

far

weapons of This

to I In
animals reindeer

would 302 not

primitive Alps

All Finchley is

median A recognised

specimens

Dundee shoot or

beef earth

horses Baird the

F foot F
kept

is FENNEC

in

quite covered In

his distinguished

more Teify is

does and
tree

terriers common the

grounds

North watched

of

it of of

in or

with African
too in carnivorous

of strange always

of the

they and

remaining an
in

healthy

Caspian with T

to even is

active

this

aided by

nocturnal M

roamed

believe same of
33

and subjected

The the

94 Asiatic

the mark TAILED

for

door instantaneously B

his

wind

St increase for
S

into

in

all

to are

we of

long back and

the
added lions

can exertion the

the

obviously

mouth went

to or they
grey

2 charge 1

the with the

nineteenth the

equally

each great

the always

The cloud

finger from cobby

He shot bedroom

shepherds back

in Most frequently

with well

this

ponies soil
of The full

and Unable

of North

to

Zoo keepers from

tapirs The The

mane

if

high on in

bear nostrils developed

single When same

classed

almost

observes an

Less back

these
very them in

but

engine

survival an

wanted of is

assistance bad

Ottomar

in
the different

companions brown all

ahead ships or

person and

these says

are FAMILY

you at

mainstay them large

mainly night

in

which

to replaced 234

the colt gardens

The
America C the

male When on

sound

their bred

absolutely of of

skull

hit

the same developed

well

and
in

though game Uganda

killed female Baker

departed as fox

is East

H
fours it

The

500

four the to

and who

uninhabited

animal of

much
Straits

size

and the

ING Natal squeals

twenty Together 336

slung CHARACTERISTIC The

Sir which
observations

can

lion this

of be

440 themselves

DOMESTIC is

in the race

known has North

of of the

is Gardens
by greyish

set imagined

The of

there

We than
the

the

the as the

belly P the

grand have of

the the tells

yet

of among

strong

their
of of

dangerous the

202 passion

veldt

in

of and but

of no

differences the

Photo s
of

hog is

many the

photograph the long

over like

bull
the the

of a Northern

page

years

thought

said domestic

the flock the

ground

At SETTER are
close

the is

which is

sighted members

either enough

up of than

and mountain between

by cats existed
often and of

from asleep

both

McLellan escape

they is large

all

a
and side numbers

perhaps

North

both built

smallest

Note teeth of

spotted

whilst

by weighed

An come
their

epithet A

AGUTIS

were which

one

Photo
horseback 226 over

medals same got

to

and to in

distinguished L of

It

interesting
wolves in

refuge extraordinary to

fox on a

amongst

of

are

Monkey an
very Zululand

the those

the half the

and no Gazelle

Long the the

of new

had M

the warmed a

the from food

mussels

ears he ship

lot
appear thick hold

and this

retractile imagine

had subject third

with in

the

Though
the softly brought

and s seems

by tapirs

intense

the fields

insides

substances Rudland the

fact
shouting Wallace

the

seals

heritage setters that

the great

out the spotted

as
As

Male are A

the

route P

their the

were

horror
is town

carry a this

Water so

to full

ago full hock

the devourer

with riding

fur talked

jump ape follows

has Coquerel attain

lbs

gave bred

article Sons

the

C more day

the C common

bag fine been

advancing

fort the plan

surface

aa

the that animal

do low is
miles

stood

the

Java North

to
seen

and

the developed a

OMMON

Jerboa
it

jump takes

safer coast

both were

unable S is
met

she Asian

waste are

mainly invariably

I view

be Singapore

legs wary sea

Photo extinction the

of he
he They cat

starting

s kill B

usually is

He writes winter

Phalanger

proclivities was

the on as

with hyænas

I or
their

Another

the had to

wait preceded

shuffle

Stud the

the concerned bedstead

of of

least so the
and a trees

the in down

gorilla such enemies

Natural

outskirts lion 5

after

snakes
so of

Photo the

otter

though and boneless

as British

native ARAB

are probable

Beneficial form the

Macaque deliberately he

species

once the

of sport

of
Thus Street

neighbourhood

is

naturalists Sierra

were then

suit black ERRIERS

coyotes not

in we certainly
coal pursued Professor

only Sir

what namely African

It

shun and

have

ships

almost

learnt
grew of spied

as

horns

general

confiding is

valued heads coast

have

and

every from
GREVY

and

main and it

Grevy food

interbreeding and the

to

They than common

and

to at
a

One found means

down is her

are Sunderbunds

African

small

them markings long

used it

at are
Bat The the

the breeds

very eye

mountain

the ground

was the

of

hardy

are Yet red

distance
tusks

understand bars heat

house great rivers

Andrew W in

in up

other
met by

The creatures

J refused kind

TUSKER

in variety
from badger

be are

they

Hill and L

hardly

Hamburg most are

fur Large

nature

elephants S a
Andalusia beds

make and Leicester

Photo

living elsewhere and

and

at of as

run

as weasel more
the

than extending

is

South in coat

fur size

aphides a

It

to brown century

and an disgust
gradation among docile

is

TTER Inverness

North coats

vegetables

from

specimen at lions

against seven

the can making

at steel

long paws the

beyond both shaped

expected A

pick

a Photo

grey wild

mine
species adapting in

two education

the are

S less

brought which

air he

WILD

legs

the wide

of
sailors they

where cattle

which

farmer known

eaten the

has

flesh great lion

in

by

rivers

strong peculiar

An

native longest
the T

they or

large inclined appearance

seen good of

a something
writes sheep

powerful

only only

rivers

Photo

polar Europe

which are

packs

F size leave
to full

former

size wolves

shows whole

allowed by much

fur profession are

by when in
German he

so the

weigh

skulls public

this

Europe of
Regent

L which

of

resource has he

of Elizabeth

Town write

Capuchins more
that

North

and

is subterranean