DNA Microarrays: A Molecular Cloning Manual

by Bowtell, David

• ISBN13: 9780879696252
• ISBN10: 0879696257
• Format: Paperback
• Copyright: 2002-10-01
• Publisher: Cold Spring Harbor Laboratory Pr

Summary

DNA microarray technology is a new and powerful means to analyze genomes and characterize patterns of gene expression. Its applications are widespread across the many fields of plant and animal biological and biomedical research. This manual, designed to extend and to complement the information in the best#x13;selling Molecular Cloning,is a synthesis of the expertise and experience of more than 30 contributors#x14;all innovators in a fast#x13;moving field. DNA Microarraysprovides authoritative, detailed instruction on the design, construction, and applications of microarrays, as well as comprehensive descriptions of the software tools and strategies required for analysis of images and data.

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 Stocks	11	(1)
PCR Amplification of Probes from Bacterial Clone Sets	12	(7)
Alternative Protocol: Preparation of Plasmid DNA as a Template for Amplification	19	(1)
Purification of PCR Products	20	(2)
Alternative Protocol: Purification of Amplified Products Using Ethanol Precipitation	22	(1)
Visualization and Assessment of PCR Products	23	(4)
Additional Protocol: Quantitation Using PicoGreen	27	(1)
Resuspending Array-ready DNA for Printing and Storing	28	(2)
Isolation and Amplification of Array Material from Yeast	30	(5)
Information Panels
Clone Sets	35	(7)
Controls Used in Spotted Microarrays	42	(3)
Prevention and Detection of Bacteriophage T1 in Genomic and cDNA Libraries	45	(4)
Spotting of Long Oligonucleotides: An Alternative to cDNA Arrays for Expression Analysis	49	(2)
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 Microarrays	68	(3)
Printing on Glass Slides	71	(8)
Checking the Quality of the Printed Slides	79	(4)
Alternative Protocol: Hybridization with Labeled Primers	83	(2)
Care and Cleaning of Quill Pens	85	(3)
Information Panels
Arrayers and Pins Used for Contact Printing of Microarrays	88	(9)
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 Cells and Tissues	110	(7)
Alternative Protocol: RNA Extraction from OCT-embedded Pathology Samples	117	(1)
Isolation of Total RNA from Tissues Using the FastPrep Instrument	118	(2)
Isolation of Total RNA from Plant Tissue using TRIzol	120	(4)
Pine Tree Method for Isolation of Plant RNA	124	(3)
Isolation of Poly(A)+ RNA Using FastTrack	127	(5)
Isolation of Membrane-bound Polysomal RNA	132	(7)
Isolation of Poly(A)+ RNA by Batch Chromatography	139	(3)
Isolation of RNA by Ultracentrifugation through CsCl Solution	142	(3)
Purification of Total RNA from Yeast	145	(3)
Alternative Protocol: Purification of RNA Using Phase Lock Gels	148	(1)
Purification of RNA from E. coli	149	(4)
Isolation and Amplification of RNA from Single Cells and Small Amounts of Tissues	153	(12)
Alternative Protocol: In Situ Transcription of RNA in Tissue Sections	165	(2)
Additional Protocol: Acridine Orange Staining of Sections	167	(1)
RNA Common Reference Sets	168	(5)
PART 2: LABELING AND HYBRIDIZATION	173	(119)
Introduction	173	(5)
Protocols
Fluorescent Labeling of First-strand cDNA Using Reverse Transcriptase	178	(8)
Alternative Protocol: Purification and Concentration of Fluorescently Labeled cDNA (Microcon YM-30)	186	(1)
Indirect Fluorescent Labeling of DNA with Amino-Allyl Dyes	187	(7)
Amplification of mRNA Preparations to Generate Targets for Screening DNA Microarrays	194	(9)
Additional Protocol: Labeling aRNA	203	(1)
Amplification of Small Quantities of mRNA for Expression Analysis	204	(10)
Labeling Second-strand DNA Using the Klenow Fragment of E. coli DNA Polymerase	214	(3)
Alternative Protocol: Labeling Genomic DNA Using the Klenow Fragment of E. coli DNA Polymerase	217	(1)
Labeling of Amplified RNA with Biotinylated Nucleotides for Hybridization to Oligonucleotide Arrays	218	(4)
Additional Protocol: Fragmentation of Biotinylated cRNA	222	(1)
Recovery of Unincorporated Cy Dyes: Repurification by HPLC	223	(5)
Hybridization and Posthybridization Washing	228	(9)
Additional Protocol: Microarray Slide Stacking	237	(3)
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 DNA	273	(1)
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 MEMBRANE ARRAY	292	(13)
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 Reuse of Membranes	303	(2)
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. Heckl
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 MICRODISSECTION	314	(17)
Introduction	314	(2)
Protocols
Manual Microdissection	316	(3)
Alternative Protocol: Microdissection of Frozen Tissue Samples	319	(1)
Laser Capture Microdissection	320	(5)
Immuno-LCM	325	(2)
Processing of Microdissected Tissue for Expression Analysis	327	(4)
PART 2: LASER PRESSURE CATAPULTING	331	(28)
Introduction	331	(7)
Protocols
Preparation of Slides for Tissue Sectioning for LPC	338	(2)
Preparation of Paraffin-embedded Tissue Sections for LMPC	340	(2)
Preparation of Sections of Fresh-Frozen Tissue for LMPC	342	(2)
LPC of Tissues Fixed in Zincfix for mRNA Profiling	344	(3)
Protection of Tissue Samples with a Liquid Coverslip	347	(2)
Isolation of Viable Cells after Laser Microdissection and Catapulting	349	(8)
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 NUMBER	359	(41)
Introduction	359	(4)
Protocols
Comparative Genomic Hybridization Using cDNA Microarrays	363	(7)
Preparation of BAC DNA for CGH by Ligation-mediated PCR	370	(10)
CGH Using BAC Genomic Microarrays	380	(6)
Microarray-based Representational Analysis of DNA Copy Number: Preparation of Target DNA	386	(8)
Microarray-based Representational Analysis of DNA Copy Number: Preparation of Slides and Hybridization	394	(6)
PART 2: MUTATION DETECTION AND SNP GENOTYPING	400	(53)
Introduction	400	(3)
Protocols
SNP Genotyping Using SBE-Tag Arrays	403	(15)
Alternative Protocol: Multiplex Amplification Reactions for SBE	418	(3)
SNP Genotyping by SBE Using Affymetrix Tag Arrays	421	(8)
Sequence Variant Detection Using High-density Microarrays	429	(10)
Loss of Heterozygosity Analysis Using SNP Arrays	439	(14)
PART 3: MICROARRAY-BASED DETECTION OF DNA-PROTEIN INTERACTIONS: CHROMATIN IMMUNOPRECIPITATION ON MICROARRAYS	453	(60)
Introduction	453	(2)
Protocols
Mapping DNA-Protein Interactions on the Yeast Genome Using Arrays	455	(5)
Mapping DNA-Protein Interactions on the Yeast Genome: DNA Amplification and Labeling	460	(5)
PART 4: SNP SEQUENCES: MAPPING DATA
Table 6-7 Multiplex Primer Pools: SNP Mapping Data	465	(28)
Table 6-8 Map Locations for SNPs on the HuSNP Chip	493	(16)
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 EXPERIMENTS	513	(13)
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 SELF-ORGANIZING MAP	582	(111)
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 of Tissue Arrays	613	(3)
In Situ Hybridization Using Tissue Arrays	616	(16)
Immunohistochemistry on Tissue Arrays	632	(11)
Alternative Protocol: Antigen Unmasking and Trypsin Digestion	643	(4)
Appendices
Appendix 1: Generation of Full-length Libraries	647	(14)
P. Carninci
Appendix 2: Reagents, Buffers, and Media	661	(22)
Appendix 3: Cautions	683	(8)
Appendix 4: Suppliers	691	(2)
Index	693