DNAマイクロアレイ:モレキュラークローニング・マニュアル<br>DNA Microarrays : A Molecular Cloning Manual

DNAマイクロアレイ:モレキュラークローニング・マニュアル
DNA Microarrays : A Molecular Cloning Manual

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  • 製本 Hardcover:ハードカバー版/ページ数 375 p.
  • 言語 ENG
  • 商品コード 9780879696245
  • DDC分類 572.86

基本説明

「モレキュラークローニング」と同様の使いやすい形態で、さらに詳細な情報を収録。
Contents: Feedstock; Making Spotted Arrays; Using Spotted Arrays for Molecular Profiling; Using Arrays for Genomic Analysis; Data Storage; Data Analysis; Downstream Validation.

Table of Contents

The DNA Microarrays Companion Web Site             xi
Preface xiii
Foreword xv
Contributors xxi
Generation of Probes for Spotted Microarrays 1 (60)
S. Chandrasekharappa
A. Holloway
V. Iyer
D. Monte
M. Murphy
N.J. Nowak
Introduction 2 (3)
Protocols
Replication and Storage of cDNA Clone Sets 5 (6)
Additional Protocol: Accessing Frozen 11 (1)
Stocks
PCR Amplification of Probes from 12 (7)
Bacterial Clone Sets
Alternative Protocol: Preparation of 19 (1)
Plasmid DNA as a Template for
Amplification
Purification of PCR Products 20 (2)
Alternative Protcol: Purification of 22 (1)
Amplified Products Using Ethanol
Precipitation
Visualization and Assessment of PCR 23 (4)
Products
Additional Protocol: Quantitation Using 27 (1)
PicoGreen
Resuspending Array-ready DNA for Printing 28 (2)
and Storing
Isolation and Amplification of Array 30 (5)
Material from Yeast
Information Panels
Clone Sets 35 (7)
Controls Used in Spotted Microarrays 42 (3)
Prevention and Detection of Bacteriophage 45 (4)
T1 in Genomic and cDNA Libraries
Spotting of Long Oligonucleotides: An 49 (2)
Alternative to cDNA Arrays for Expression
Analysis
Yeast Probes 51 (10)
Printing Spotted Glass Microarrays 61 (40)
G. Childs
J. DeRisi
T. Harris
A. Holloway
B.-H. Hou
A. Massimi
M. Murphy
S. Somerville
Introduction 61 (7)
Protocols
Preparing Poly-L-Lysine Slides for 68 (3)
Microarrays
Printing on Glass Slides 71 (8)
Checking the Quality of the Printed Slides 79 (4)
Alternative Protocol: Hybridization with 83 (2)
Labeled Primers
Care and Cleaning of Quill Pens 85 (3)
Information Panels
Arrayers and Pins Used for Contact Printing 88 (9)
of Microarrays
Substrates for Printing 97 (4)
Expression Analysis of RNA 101 (3)
M. Bittner
R. Butow
J. DeRisi
M. Diehn
J. Eberwine
C.B. Epstein
R. Glynne
S. Grimmond
T. Ideker
J.E. Kacharmina
S. Katsabanis
J. Khan
J. Lee
C.L. Liu
P. Marciano
F.M. Marincola
T. McIntosh
D. Monte
J.R. Pollack
V. Rhodius
S. Somerville
E. Tom
E. Wang
J.S. Wei
D. Willhite
S. Ybarra
Introduction 102 (2)
PART 1: ISOLATING RNA 104 (69)
Introduction 104 (6)
Protocols
Purification of Total RNA from Mammalian 110 (7)
Cells and Tissues
Alternative Protocol: RNA Extraction from 117 (1)
OCT-embedded Pathology Samples
Isolation of Total RNA from Tissues Using 118 (2)
the FastPrep Instrument
Isolation of Total RNA from Plant Tissue 120 (4)
Using TRIzol
Pine Tree Method for Isolation of Plant 124 (3)
RNA
Isolation of Poly(A)+ RNA Using FastTrack 127 (5)
Isolation of Membrane-bound Polysomal RNA 132 (7)
Isolation of Poly(A)+ RNA by Batch 139 (3)
Chromatography
Isolation of RNA by Ultracentrifugation 142 (3)
through CsCl Solution
Purification of Total RNA from Yeast 145 (3)
Alternative Protocol: Purification of RNA 148 (1)
Using Phase Lock Gels
Purification of RNA from E. coli 149 (4)
Isolation and Amplification of RNA from 153 (12)
Single Cells and Small Amounts of Tissues
Alternative Protocol: In Situ 165 (2)
Transcription of RNA in Tissue Sections
Additional Protocol: Acridine Orange 167 (1)
Staining of Sections
RNA Common Reference Sets 168 (5)
PART 2: LABELING AND HYBRIDIZATION 173 (119)
Introduction 173 (5)
Protocols
Fluorescent Labeling of First-strand cDNA 178 (8)
Using Reverse Transcriptase
Alternative Protocol: Purification and 186 (1)
Concentration of Fluorescently Labeled
cDNA (Microcon YM-30)
Indirect Fluorescent Labeling of DNA with 187 (7)
Amino-Allyl Dyes
Amplification of mRNA Preparations to 194 (9)
Generate Targets for Screening DNA
Microarrays
Additional Protocol: Labeling aRNA 203 (1)
Amplification of Small Quantities of mRNA 204 (10)
for Expression Analysis
Labeling Second-strand DNA Using the 214 (3)
Klenow Fragment of E. coli DNA Polymerase
Alternative Protocol: Labeling Genomic 217 (1)
DNA Using the Klenow Fragment of E. coli
DNA Polymerase
Labeling of Amplified RNA with 218 (4)
Biotinylated Nucleotides for
Hybridization to Oligonucleotide Arrays
Additional Protocol: Fragmentation of 222 (1)
Biotinylated cRNA
Recovery of Unincorporated Cy Dyes: 223 (5)
Repurification by HPLC
Hybridization and Posthybridization 228 (9)
Washing
Additional Protocol: Microarray Slide 237 (3)
Stacking
Troubleshooting Guide 240 (17)
Information Panels
Alexa Dyes 257 (2)
Bacterial Microarrays 259 (2)
Extraction of Proteins and DNA with Phenol 261 (2)
Formamide 263 (2)
Guanidinium-based Extraction of RNA 265 (1)
Homogenization of Animal Cells and Tissues 266 (2)
Inhibiting RNases 268 (2)
Mammalian, Plant, and Bacterial RNAs 270 (3)
Measuring the Efficiency of Dye Labeling of 273 (1)
DNA
Moloney Leukemia Virus Reverse Transcriptase 274 (1)
Oligo(dT)-Cellulose 275 (1)
Quantification of RNA 276 (1)
Special Considerations for Working with RNA 277 (2)
Storage and Recovery of RNA 279 (10)
Membrane-based Spotted cDNA Arrays 289 (3)
K.G. Becker
W.H. Wood III
C. Cheadle
Introduction 289 (3)
PART 1: PREPARATION AND HYBRIDIZATION OF 292 (13)
MEMBRANE ARRAY
Protocols
Printing Membrane Arrays 293 (4)
RNA Preparation and Labeling 297 (3)
Hybridization of Target to Membrane Arrays 300 (3)
Additional Protocol: Target Stripping and 303 (2)
Reuse of Membranes
PART 2: DATA ANALYSIS AND INTERPRETATION 305 (9)
Tissue Microdissection 307 (7)
B. Becker
M. Bernsen
C.J.M. Best
T. Bjornsen
D. Brocksch
R. Burgemeister
C. Bush
R.F. Chuaqui
A. Clement-Sengewald
M.R. Emmert-Buck
G. Friedemann
J.W. Gillespie
W. Hackel
G. Lahr
I.M. Leiva
P. Lindahl
A. Mayer
S. Nilsson
K. Schutze
S.J. Sheidl
M. Stich
W. Stolz
M. Takemoto
S. Thalhammer
M.C.R.F van Dijk
T. Vogt
Introduction 308 (6)
PART 1: MANUAL DISSECTION AND LASER CAPTURE 314 (17)
MICRODISSECTION
Introduction 314 (2)
Protocols
Manual Microdissection 316 (3)
Alternative Protocol: Microdissection of 319 (1)
Frozen Tissue Samples
Laser Capture Microdissection 320 (5)
Immuno-LCM 325 (2)
Processing of Microdissected Tissue for 327 (4)
Expression Analysis
PART 2: LASER PRESSURE CATAPULTING 331 (28)
Introduction 331 (7)
Protocols
Preparation of Slides for Tissue 338 (2)
Sectioning for LPC
Preparation of Paraffin-embedded Tissue 340 (2)
Sections for LMPC
Preparation of Sections of Fresh-Frozen 342 (2)
Tissue for LMPC
LPC of Tissues Fixed in Zincfix for mRNA 344 (3)
Profiling
Protection of Tissue Samples with a 347 (2)
Liquid Coverslip
Isolation of Viable Cells after Laser 349 (8)
Microdissection and Catapulting
Using Microarrays for Genomic Analysis 357 (2)
D. Albertson
S. Dee
J.-B. Fan
J.N. Hirschhorn
X. Huang
V. Iyer
Y.-M. Lim
K. Lindblad-Toh
R. Lucito
H. Matsuzaki
N. Patil
D. Pinkel
J.R. Pollack
T. Ryder
R. Segraves
P. Sklar
A. Snijders
M. Wigler
Introduction 358 (1)
PART 1: MICROARRAY-BASED DETECTION OF DNA COPY 359 (41)
NUMBER
Introduction 259 (104)
Protocols
Comparative Genomic Hybridization Using 363 (7)
cDNA Microarrays
Preparation of BAC DNA for CGH by 370 (10)
Ligation-mediated PCR
CGH Using BAC Genomic Microarrays 380 (6)
Microarray-based Representational 386 (8)
Analysis of DNA Copy Number: Preparation
of Target DNA
Microarray-based Representational 394 (6)
Analysis of DNA Copy Number: Preparation
of Slides and Hybridization
PART 2: MUTATION DETECTION AND SNP GENOTYPING 400 (53)
Introduction 400 (3)
Protocols
SNP Genotyping Using SBE-Tag Arrays 403 (15)
Alternative Protocol: Multiplex 418 (3)
Amplification Reactions for SBE
SNP Genotyping by SBE Using Affymetrix 421 (8)
Tag Arrays
Sequence Variant Detection Using 429 (10)
High-density Microarrays
Loss of Heterozygosity Analysis Using SNP 439 (14)
Arrays
PART 3: MICROARRAY-BASED DETECTION OF 453 (60)
DNA-PROTEIN INTERACTIONS: CHROMATIN
IMMUNOPRECIPITATION ON MICROARRAYS
Introduction 453 (2)
Protocols
Mapping DNA-Protein Interactions on the 455 (5)
Yeast Genome Using Arrays
Mapping DNA-Protein Interactions on the 460 (5)
Yeast Genome: DNA Amplification and
Labeling
PART 4: SNP SEQUENCES: MAPPING DATA
Table 6-7 Multiplex Primer Pools: SNP 465 (28)
Mapping Data
Table 6-8 Map Locations for SNPs on the 493 (16)
HuSNP Chip
An Introduction to Microarray Bioinformatics 509 (4)
C.A. Ball
Y. Chen
S. Panavally
G. Sherlock
T. Speed
P.T. Spellman
Y.H. Yang
Introduction 509 (4)
PART 1: DESIGN OF MICROARRAY EXPRESSION 513 (13)
EXPERIMENTS
PART 2: IMAGE ANALYSIS 526 (10)
PART 3: NORMALIZATION 536 (8)
PART 4: REPRESENTING AND EVALUATING SLIDE DATA 544 (8)
PART 5: LIMS, DATABASES, AND DATA MANAGEMENT 552 (17)
PART 6: CLUSTER ANALYSIS AND DISPLAY 569 (13)
PART 7: MULTIDIMENSIONAL SCALING AND 582 (111)
SELF-ORGANIZING MAP
Information Panels
Gene Annotation 590 (4)
Sharing Microarray Data among Investigators 594 (9)
Tissue Microarrays 603 (90)
K. Brand
G. Hostetter
O.-P. Kallioniemi
J. Kononen
G. Sauter
M. Trivett
Introduction 603 (5)
Protocols
Construction of Tissue Microarrays 608 (5)
Additional Protocol: Manual Construction 613 (3)
of Tissue Arrays
In Situ Hybridization Using Tissue Arrays 616 (16)
Immunohistochemistry on Tissue Arrays 632 (11)
Alternative Protocol: Antigen Unmasking 643 (4)
and Trypsin Digestion
Appendices
Appendix 1: Generation of Full-length 647 (14)
Libraries
P. Carninci
Appendix 2: Reagents, Buffers, and Media 661 (22)
Appendix 3: Cautions 683 (8)
Appendix 4: Suppliers 691 (2)
Index 693