Microarray

Background Hardware     Arrayer/ Spotter     Scanner     Microarray slide (pre-spotted)     Accessaries     Microdissection     Alternative array technologies Software Analysis Protocols    Trouble Shooting Protein Chip/ SELDI-TOF-MS Tissue Microarray (TMA)    Hardware    Software    TMA slides (pre-made)

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Background

• A movie shows the experimental steps involved in the generation of high-throughput gene expression data from tissues using cDNA
  
microarrays.
• ABRF MICROARRAY RESEARCH GROUP STUDY: A CURRENT PROFILE OF MICROARRAY LABORATORIES 2001 - A survey performed by The Microarray Research Group, The Association of Biomolecular Resource Facilities (ABRF). You can find the summary of the result here. The year 2000 survery is available here.
• An Introduction to DNA Microarray Technology - a presentation of microarray technology
• Anatomy of a Comparative Gene Expression Study  - concise and good review of microarray technology
• DNA Microarrays and Expression Bioinformatics - a clear and concise review by Viraphong Lulitanond.
• DNA Microarray Methodology - Flash Animation  - interesting cartoon for the basis of microarray experiment, flash player is required to play the file
• DNA Microarray (Genome Chip)  - a good review of many aspects of microarray technologies
• GENE ARRAYS - a simple introduction of microarray from beginning to the end
• Microarray and "DNA chips" -  an excellent microarray resources maintained by The Pharmaceutical Research and Manufacturers of America and the PhRMA Foundation
• Microarray Centre at The Ontario Cancer Institute, University Health Network General Overview & Hybridization Tutorial.
• Microarray Fact Sheets @ NCBI - A comprehensive introduction of microarray technology
  
• NRC-BRI Microarray Lab Flash movies - excellent flash movies introducing various step of microarray analysis

Hardware

Array of Options - a instrumental review by the Scientist.
Guide to microarray hardware  - a researcher perspective - A review article on hardware writtern by me in 2001 :P; hosted in  lab-on-a-chip.com. HOT!!!
Options available-from start to finish-for obtaining data from DNA microarrays II. Nat Genet. 2002 Dec;32 Suppl 2:481-9. A very recent review article   by Holloway AJ, Van Laar RK, Tothill RW, Bowtell DD. [PubMed][pdf][web supplement]

Arrayer/ Spotter

• Affymetrix 417 arrayer - Previously known as Genetic MicroSystem. Affymetrix bought its technologies to conquer the low-end market. Its proprietary Pin-and-Ring arraying mechanism allows you to array even spots among arrays.
• Agilent arrayer - manufactured by Agilent. An inkjet arrayer capable for arraying cDNA and synthesize oligos in situ.
• Cartesian Technologies - It provides both contact and non-contact platform with various printing capacities.
• GeneMachines OmniGrid & Accent - Manufactured by GeneMachines
• GeneTac G3 Robotic Workstation - Arrayer system from Genomic Solutions
• Glass Slide Microarrayer -  an economic manual system to array 768 spots/ slide by V&P scientific. It has many accessoriesthat makes manual arraying easier.
• Intelligent Bio-Instruments - making a high throughput automated microarrayer
• Lucidea Array Spotter - Manufactured by Amersham Bioscience
• MicroGrid I & II -  Manufactured by Biorobotics
• MicroCASTer - manual arrayer system from Schleicher & Schuell; the main unit is the same as V&P scientific.
• Nano-Plotter NP 1.2 - a piezoelectric tips microarraying system manufactured by GeSiM mbH.
• Packard Biochip Arrayer - Manufactured by Packard Biocip Technologies.
• QArray2; QArray mini; QArrayMax - Manufactured by  Genetix
• RoboArrayer- A fully integrated Micro Arrayer complete with digital vision inspection by RoboDesign. Capable of speeds up to 15360 spots per hour
• sciFLEXARRAYER - An ultra low volume, non-contact drop on demand dispenser manufactured by SCIENION, typical transfer volumes are between 100 pl to 5 nl.
  
• SPBIO Microarray Spotter - Manufactured by MiraiBio Inc.
• SpotBot - A personal microarrayer manufactured by arrayit.com
• VersArray Colony Picker and Arrayer Systems - Arrayer system that can array on either glass slides or membrane manufactured by Bio-Rad; previously known as SDDC system by ESI and manufactured by Virtek Vision International.

Scanner

• aQuire - Scanner system from Genetix.
  
• Affymetrix 418 & 428 scanners - Previously known as Genetic MicroSystem. Affymetrix bought its technologies to conquer the low-end market. The highest resolution is 10 microns
• Agilent DNA microarray scanner - 2 lasers scanner system by Agilent; The highest resolution is 5 microns; capable of loading 48 slides with autoloader.
• Applied Biosystems 1700 Chemiluminescent Microarray Analyzer - based on chemiluminescence rather than fluorescence detection
  
• ArrayTube AT Reader - a specialized reader for reading ArrayTube AT system, a genotyping and SNP analysis products manufactured by Clondiag;
• arrayWoRx - A CCD scanner system from Applied Precision. The highest resolution is 5 microns.
• DNAscope Mark II & Open Frame Research DNAscope - a confocal scanner system from GeneFocus. The highest resolution is 5 microns; the open frame research DNAscope is designed specifically for research and development of new microarray technologies. GeneFocus claims it is proved particularly effective for imaging Affymetrix GeneChips.
• GeneChip® Instrument System - Scanner for high-density photolithographic synthesized oligo arrays from Affymetrix.
  
• GenePix Professional 4200A & 4200AL, 4000B & Personal 4100A - These microarray scanners are manufactured by Axon Instruments, Inc. They are compact and user-friendly machines. A wide-range of publications used GenePix as their scanning platform. The highest resolution is 5 microns. Refer to their comparison table to see the difference between their scanners.
  
• GeneTac 2000 & LS IV - Scanner systems from Genomic Solutions
• Genorama Detector - Scanner system from Asper Biotech
• ScanArray - Previously manufactured by GSI-Lumonics, a company focused in laser-based advanced manufacturing systems and components. There is optional multi-loader and bar-code system for high volume array scanning. The highest resolution is 5 microns.
• Typhoon 9410 - a high performance gel and blot imager with the capability of microarray analysis; manufactured by Amersham Biosciences.
• VersArray ChipReader - A compact scanner manufactured by Bio-Rad, previously by Virtek Vision International.
  

Microarray slide (pre-spotted)

• Agilent Human Catalog Oligo & cDNA Microarray Kit - manufactured by Agilent; An invaluable resources for those who have been using incyte genomics' array and greatly affected by their recently decision of quiting from array business. oligos array products include: Human 1A Oligo Microarray Kit  (22,000 unique 60-mer oligos representing over 17,000 unique human genes sourced from Incyte's Genomics Foundation Database); Mouse (Development) Oligo Microarray Kit (20,000 unique 60-mer oligos representing sequences derived from the NIA/NIH cDNA mouse clone set); Yeast Oligo Microarray Kit  (10,000 unique 60-mer oligos representing more than 6,250 ORFs from the Saccharomyces Genome Database 25-May-2002 ORF list) Arabidopsis 1 Oligonucleotide Microarray Kit (14,800 unique 60-mer oligos representing sequences from the TIGR Arabidopsis thaliana Database). cDNA array products include: Human 1 cDNA Microarray Kit (12,000 Incyte's Human Drug Target and UniGene Clones); Human 2 cDNA Microarray Kit (14,000 Incyte Human Foundation 1 & 2 Clone Sets.); Mouse cDNA Microarray Kit (8,500 unique clones from  Incyte's Mouse UniGene 1 Clone Set); Rat cDNA Microarray Kit (14,500 unique clones from Incyte's Genomic Rat Toxicology and Foundation 1 Clone Sets).
• Applied Biosystems genome survey array - human (30,000 genes) and mouse (32,000 genes)
  
• Atlas glass microarray - manufactured by Clontech; products include: Human 3.8 (3,800 genes), Human 1.0 (1,081 genes), Mouse 3.8,Mouse 1.0 and Rat 1.0 array.
• ArrayTube AT system - a genotyping and SNP analysis products manufactured by Clondiag; products include: cyp2D6 gene genotyping; Staphylococcus aureus resistance genotyping.
• Biodoor microarray - manufactured by Biowindow, a subsidiary of United Gene Holdings, one of the largest Chinese biotech company; products: general human and mouse gene expression arrays with spot density from 500 to 12800. Specialty arrays (classified gene expression arrays) include oncogenes & tumor suppressor genes, ion channels & transport proteins, cell cycle control proteins, cytoskeleton & motility, apoptosis & hypersensitivity proteins, DNA synthesis, repair and recombination,  cell receptor, immunity, signal transduction, metabolism, protein translation and synthesis, growth related. Disease management arrays including liver cancer related and lung cancer related arrays.
• CombiMatrix CustomArray - custom slide format oligo microarrays from CombiMatrix with 902 (~$400) or 12000 genes (~$550), synthesized using an electrochemical detritylation method. There are no set-up fees, no minimum orders, and there is free bioinformatics for probe design.
  
• discoveryARRAY - from Q-BIO gene; products include human and mousearray.
• Discovery Microarray (3,600 genes) & Control Microarray - manufactured by Stratagene's GeneConnection; products include a EST array for novel gene finding.
• ExpressChip - 30mers oligos chip of human, mouse and rat manufactured by Mergen for expression profiling
• GeneChip Arrays - GeneChip probe arrays for gene expression and DNA analysis manufactured by Affymetrix.
  
• GeneMap microarray - manufactured by Genomic Solutions; products include human (1,152 genes), mouse (992 genes) and rat (1,700 genes).
• HOTSPOT cDNA Microarray - manufactured by Genotypic Technology; products include Human Select 2304 (2,304 human genes duplicated), Human 10K, Human Cancer select, Human Function Specific Arrays for Apoptosis and Cell Cycle.
  
• Human RNA Chip - manufactured by Clontech; consists of 124 human fetal and adult tissue-specific Poly A+ RNAs, including 20 RNAs derived from different tumor cell lines. Useful for testing gene expression level across different tissues.
• Intelligene microarray - manufactured by Takara Shuzo; products include: Arabidopsis (2,200 genes), Photosynthesis mechanism (2,800 genes), E.Coli (4,000 genes), Human Apoptosis (164 genes), Human (1,000 genes),  Human Cancer (630 genes), Human Cytokine (240 genes), Human stem cells (370 genes), Human endocrine disruption (240 genes), Mouse (600 genes) and practice array (90 genes).
• Microarrays service by Microarray Centre at The Ontario Cancer Institute, University Health Network - the centre works on a not-for-profit basis to provide microarrays, products include: Human 1.7K (1,700 ESTs), Human 19K (19,000 ESTs), Mouse 15K (15,000 ESTs) and Yeast ORF (6,200 ESTs). The gene list of different product is available here.
• MicroMax microarray - manufactured by Perkin Elmer; products include: screening array 1.1 - 4800 genes (2400 genes of version 1 spotted in duplicate) with direct or TSA labelling, screening array 2 with TSA labelling (4800 genes containing sequence-verified Human Drug Target Genes mined from Incyte Genomics' LifeSeq® Gold database); focus arrays like Human Kinases and Phosphatases (275 genes), Human Transcription Factors (321 genes), Human Oncogenes and Tumor Suppresor Genes (325 genes) and Human Ion Channel, Transporter and Receptor Genes arrays (299 genes) and practice/ control array. Coming soon Human Neurobiology Genes Array & Human Apoptosis Genes Array.
• MWG catalog arrays - 40-50mer oligos array manfactured by MWG Biotech; products include:  Human 30k Array; Human 10k Array A; Human 10k Array B; Human 10k Array C; Chromosome 21 Array; Human Cancer Array; Rat 5k / 10K Array; Mouse 30k Array; Mouse 10k A Array; Mouse 10k B Array; Mouse 10k C Array; Zebrafish 14k Array; Rat Liver Array; MWG Yeast Array; MWGE. coli K12 Array; MWGHelicobacter pylori Array; MWGStreptococcus pneumoniae Array; MWGCampylobacter jejunii Array; MWGE. coli Starter Kit; MWG Human Starter Array.
  
• OpArrays - 70 mers oligos array manufactured by Operon Technologies; products include: Human Collage OpArray (328 genes), Human Cancer OpArray (1,168 genes), Human Apoptosis OpArray (384 genes), Human Stress and Aging OpArray (693 genes), Yeast Collage OpArray (372 genes).
• sciTRACER arrays - manufactured by SCIENION; products include :Inflammation 430, Cardio Vascular 725, and Disease.
• SpectralChip-Human & Mouse BAC Array - manufactured by Spectral Genomics;  The human and mouse array contains 1003 and 976 non-overlapping BAC clones respectively from RPCI BAC library spotted in duplicate. The BACs span the genome at approximately 3 Mb intervals, which enables the detection of aberrations greater than 3 Mb.
• Stanford Functional Genomics Facility arrays - The core facility at stanford providing 42,000 elements mouse and human array at US$95, including web based bioinformatic support from the Stanford Microarray Database.
  
• Toxicology Microarray - manufactured by Phase-1Molecular Toxicology; products include human, canine, rat and custom arrays to efficiently address toxicologically-relevant gene pathways.
  

Accessaries (pins, DNA clones, oligos for arraying, control RNA, glass slide, RNA purification, quality accessment, labeling and amplication, etc.)

Array pins

• Genetix tungsten aQu microarray spotting pins - spotting pins provided by Genetix.
• Silicon Microarray Technology - a microcontact printing pin manufactured by micromachined crystal silicon. Product of Parallel Synthesis Technologies.
  

cDNA synthesis kit

• SOLIDscript Solid Phase cDNA Synthesis Kit - purify RNA and make immobilized cDNA library in  less than 2 hours and suitable for subsequent aRNA amplification, manufactured by  CPG Inc.

cDNA product/ clones/ oligos for arraying

• Array-Ready Oligo sets - oligos for arraying by Operon technologies.
• arrayTAG - a family of cDNA clone collections, specifically designed for microarrays by Lion Bioscience. Currently mouse, rat and dog are available. arrayTAG is directly linked to the integrated annotation database arrayBASE and microarray analysis software arraySCOUT  to speed up the access to in-depth information about the differentially expressed genes.
• ATCC (American Type Culture Collection) - providing Mammalian Gene Collection (MGC), I.M.A.G.E. consortium clones and NIA/NIH Mouse cDNA collection.
• Atlas Ready-to-print Long Oligos - 80 base long oligos of human (5,278 genes), mouse (3,197 genes) and rat (2,727 genes)  for printing 1000/ 2500 microarrays from Clontech.
• Cellex cDNAs - cDNAS from various neuron subtypes of mouse, dissected by LCM. Products of Arcturus
• Easy to spot products - sequence verified huamn, mouse, arabidopsis and drosophila PCR products from Incyte Genomics.
• Full length Human Gene Resources - Full length human cDNA clones from Research Genetics.
• GeneConnection Discovery clone collection & QuikSpot PCR products - 33,000 sequence verified clones from 29 human tissues available in clones or PCR format for arraying by Stratagene.
• GenScript Custom Oligos and Gene Synthesis - Large scale production of cDNA fragments for microarray using de novo gene synthesis, and high-purity oligos for microarray.
  
• Mammalian Gene Collection (MGC) - The goal of the Mammalian Gene Collection (MGC) is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse. The MGC is an NIH initiative that supports the production of cDNA libraries, clones and sequences. All the resources generated by the MGC are publicly accessible to the biomedical research community.
• MWG oligo sets - 40-50mer probes for arraying. products including yeast, E.Coli, H. Pylori, rat, mouse, zebrafish, human cancer and human.
  
• My Array DNA 1000 & 2000 - array ready PCR products/ with clones from Research Genetics.
• NIA/NIH Mouse Genomics Home Page
• Oligonucleotide Sequences for Human and Mouse RNA Assays - An open-source oligomicroarray standard for human and mouse offered by Harvard-Lipper Center for Computational Genetics. Reference [PubMed]
• Open Biosystems Clones - including  I.M.A.G.E./MGC cDNA Clones,  C. elegans ORF clones and Incyte cDNA Clones and Libraries.
  
• OriGene Human Full-Length cDNA clones - 10,000 full-length "cDNA clones" whose nucleotide sequences can be found in the public domain.
• sciOLIGOs-  ready-to-spot long-mer oligonucleotides (60-70 nt) designed specifically for genes of interest, manufactured by SCIENION;
• RefSet oligos for the human genome - contains 22,740 70mer oligonucleotide probes targeting 20,726 characterized genes in the human genome. Product of Illumina.
  
• Research Genetics Full Length Human Gene Resources - providing over 35,000 cDNA clones and NIH Mammalian Gene Collection (MGC) clones.
• UK HGMP-RC I.M.A.G.E. Consortium cDNA libraray -  Biological resources from UK Human Genome Mapping Project Resource Centre.

Control mRNA and PCR products

• Lucidea ScoreCard Platform - a set of 23 artificial genes from yeast intergenic regions that serve as analytical controls to validate, filter, and normalize microarray data; manufactured by Amersham Biosciences
• SpotReport Array Validation System - is a group of controls that collectively validate experimental parameters for microarray system; manufactured by Stratagene.
• Universal Human Reference RNA - Total RNA prepared from 10 different cell lines and use as an universal reference in microarray experiment.

Fluorescence Image Standard

• FluorIS - An array imaging standardization tool by using almost non bleaching fluorescent spots defined in shape and intensity. Useful for calibration and normalization purposes. Allows the direct comparison of array images generated by different fluorescence reader systems or a single detection system at different time intervals; manufactured by Clondiag.

Glass slides (blank)

• Asper Biotech Coated Slides - glass slides with various coating by Asper Biotech
• Bioslide pre-coated slides - glass slides manufactured by Bioslide
• CMT-GAPS Coated Slides - glass slides manufactured by Corning Microarray Technology.
• DNA-Ready Type I & II Slides - glass slides manufacture by Clontech.
• EZ-RAYS - Universal Activated Slide Kits for spotted DNA microarrays by Apogent Discoveries
• FAST& CAST slides - glass slides manufactured by Schleicher & Schuell
• Genetix glass slides - glass slides provided by Genetix
• Microarray slides & Lifter Slips- glass slides & cover slip manufactured by Erie Scientific.
• Nexterion Slide - glass slides manufactured by Schott Glas
  
• Quantifoil Microarray Technology - glass slides of epoxy, aldehyde and amino modifide coating by Quantifoil.
• SuperStrate - a dual layer broadband-enhanced surface for improved signal to noise in most microarray reading systems manufactured by bioDevice.

Hybridization chamber/ system

• Agilent Hybridization Chambers - hybridization chambers for Agilent microarrays.
• Array Booster - hybridization chambers using surface acoustic waves (SAW) to effectively agitate the sample solution during the incubation of DNA- or protein microarrays, product of Advalytix AG.
  
• Atlas Glass Hybridization Chamber and solution - hybridization chamber and solution manufactured by clontech.
• CMT-Hybridization Chamber - hybridization chamber manufactured by Corning Microarray Technology.
• Genetix Hybridisation Chamber and GenHYB microarray hybridisation solution - hybridization chamber, hybridization solution manufactured by Genetix
  
• GeneTAC Hybridization Station - An automated system for processing biochips manufactured by Genomic Solutions.
• QUANTIFOIL Hybridization systems - hybridization chambers and systems manufactured by QUANTIFOIL Instruments.
• Lucidea Automated Slide Processor - allows automation of microarray slide processing, including prehybridization, hybridization, and washing; manufactured by Amersham Bioscience.
• MAUI Hybridization System -  A low-volume, active-mixing hybridization chamber manufactured by BioMicro Systems.
• sciHYBCHAMBER - A hybridization chamber manufactured by SCIENION.
• Ventana Discovery - an automated system for microarray, ISH, IHC and FISH processing; manufactured by Ventana Medical Systems.
  

Labelling kit

• 3DNA Detection systems - A labelling kit from Genispherethat can detect microgram level of total RNA reliably.
• Agilent Microarray Labeling & Hybridization Reagent Kits - various types of labelling kits manufactured by Agilent.
• Atlas Glass Fluorescent Labeling Kit - a labelling kit manufactured by Clontech.
• arrayTRACKER standard and low-RNA labelling kit - labelling kits from Q-BIO gene.
• CyScribe cDNA labelling kits - First-Strand cDNA labelling kit and Post-Labelling kit manufactured by Amersham Biosciences.
• Direct Microarray Labelling kitand FairPlay Microarray Labelling kit - labelling kits from Stratagene.
• ENZO Life Sciences Microarray Products - labelling kits from Enzo Life Sciences
  
• HC ExpressArray Kit - provides rapid, highly sensitive and reproducible quantitative detection of gene expression on microarrays. The technology is based on a universal hybridization and detection technology which utilizes a patented antibody specific for RNA:DNA hybrids coupled with fluorescent signal amplification. Manufactured by Digene.
• HySpot cDNA or PCR labelling kit - manufactured by Genetix
• MICROMAX Direct Reagent Kit regular & large- a labelling kit manufactured by Perkin Elmer.
• MICROMAX TSA Labeling and Detection Kits - TSA signal amplification kit manufactured by Perkin Elmer.

Quality checking

• SpotCheck -  Microarray Slide QC Kit manufactured by Genetix.

RNA purification

• Atlas Glass Total RNA Isolation Kit - total RNA isolation kit manufactured by Clontech.
• mVADER systems - various RNA purification systems manufactured by Active Motif.
• RNA purification systems - various RNA purification systems manufactured by  CPG Inc.

RNA quality accessment

• Agilent 2100 Bioanalyzer - accessing RNA quality by RNA LabChip^® Kits before labeling reactions

RNA amplication

• ExpressArt™ mRNA Amplification Kit - RNA amplification kit manufactured by Artus GmbH.
  
• MessageAmp™ aRNA Kit - RNA amplification based on Eberwine method, manufactured by Ambion.
• RiboAmp RNA Amplification Kit (for few nanograms of total RNA), RiboAmp HS RNA Amplification Kit (for few hundred picograms of total RNA) & RiboAmp OA RNA Amplification Kit (amplication kit for oligonucleotide arrays) - RNA amplification kit manufactured by Arcturus.

RNA labeling quality accessment

• Nanodrop - cuvette free spectrophotometer for labeling quality accessment

Solution

• Amine and Aldehyde Spotting Solutions - Solutions provided by Genetix
  
• Quantifoil solutions and Buffers - spotting, blocking and hybridization buffers manufactured by Quantifoil.

Microdissection

• P.A.L.M. (Positioning and Ablation with Laser- MicroBeams) - Laser Microbeam Microdissection (LMM) & Laser Pressure Catapulting (LPC) for contamination free microdissection by P.A.L.M. Mikrolaser Technologie
• AutoPix and PixCell IIe - Laser Capture Microdissection (LCM) systems by Arcturus Engineering, Inc
• HistoGene LCM Frozen Section Staining Kit - prepares frozen tissue for LCM while maintaining high-quality RNA
• HistoGene LCM Immunofluorescence Staining Kits - preserves RNA integrity during immunofluorescence processing.
• PicoPure DNA Extraction Kit -  prepares PCR-ready DNA
• PicoPure RNA Isolation Kit
  
• RiboAmpRNA Amplification Kit
  
• RiboAmp HS RNA Amplification Kit
  
• RiboAmp OA RNA Amplification Kit

Alternative array technologies

Software

• Chih Long Liu's Web Site 
• Clustering Calculator - An online clustering program with comprehensive explanations of the distance measures and clustering algorithms.
• microarray.org  - A good portal of microarray softwares; most of the freewares for microarray analysis are available here
• R Packages For Gene Expression Analysis - One of the most completed lists for array analysis R packages, maintained by Dr. Korbinian Strimmer.
• The Brown Lab - arrayer software download

Analysis

• An overview of Transformation and Normalization techniques
  
• Electronic Statistics Textbook
  
• Gene Networks from Microarray Data - a Literature Thesis by Bas Dutilh, Utrecht University; html format, pdf format.
• NHGRI microarray project analysis online tutorial - comprehensive discussion of image analysis, data visualization and mining, database construction etc.
• Recommendations for analysis of microrray data - Some tips for analyzing microarray data from clinical research.
• Rice Virtual Lab in Statistics
  

Protocols

• ADGE Microarray - The ADGE (Amplified Differential Gene Expression) method was designed to quadratically magnify the ratios of genes with the integration of DNA reassociation and PCR. ADGE microarray is the combination of the ADGE technique and DNA microarray.
  
• AECOM Microarray protocols
• aRNA amplification
• Arabidopsis Functional Genomics Consortium (AFGC) Microarray Services RNA Isolation Protocols - Various protocols for isolating RNA from most plant tissue
• Array-it.com DNA microarray protocols  - A very detail protocol from preparation of DNA to hybridization. There are also a short protocols for gene expression analysis and mutation detection with oligo microarrays
• Bauer Center for Genomics Research, Harvard University Protocols
  
• Bayer College of Medicine Microarray Core Facility Protocols
• Chih Long Liu's Web Site -  Chih Long Liu is currently a Stanford alumnus ('01, Biological Sciences) and a Harvard graduate student in the BBS PhD program. He is a former Brown Lab member (Biochemistry Department) and initially joined the lab in the summer of 1998 with the development of the cy dye repurification protocol.
• microarray.org - A huge collection of the protocols from the beginning to the end of your experiment!All are in pdf!
• Microarray Centre at The Ontario Cancer Institute, University Health Network Protocols & Tutorial
  
• Lindahl Group Protocol at The Sahlgrenska Academy - A few very useful protocols on Laser Microbeam Microdissection (LMM) & Laser Pressure Catapulting (LPC), RNA amplification and microarray hybridization.
• Modified Eberwine aRNA amplification protocol
• NHGRI microarray project protocols  - It is a very good and detailed protocols from the preparation of your DNA samples to spotting and hybridizing your slide, I recommend to download the pdf version
• Protocols Online - Microarray Protocols - A very comprehensive collection of contemporary microarray protocols available online, maintained by Long-Cheng Li.
  
• Protocols for making Drosophila arrays
• The Brown Lab - Experimental protocols - Dr. Patrick Brown is a famous person in microarray field, his homepage provides the protocols for doing your microarray experiment
• Yeast genomic expression studies using DNA microarrays - A very detailed step-by-step review on the experimental protocols and considerations, written by Dr. Audrey Gasch for Methods in Enzymology Vol 350: Guide to Yeast Genetics and Molecular and Cellular Biology. Reference [PubMed][pdf]
  

Trouble Shooting

• Microarray troubleshooting - An image gallery of common problems during microarray experiment and the respective solutions
• Trouble-Shooting Guide - Another image gallery of  common problems during microarray experiment and the respective solutions
  

Protein Chip/ SELDI-TOF-MS

• Ciphergen - one of the first company to produce commercial protein chip platform, based on SELDI-TOF-MS technology.
• ZYOMYX - developing technologies for manufacturing protein biochips

Tissue Microarray (TMA)

• Association for Pathology Informatics (API) - The Mission of the Association for Pathology Informatics (API) is to promote the field of pathology informatics as an academic and a clinical subspecialty of pathology.
  
• Johns Hopkins Pathology Tissue Microarray Core
  
• NHGRI tissue microarray project
• PMCI Tissue Array Facility
• Stanford Tissue Microarray Consortium Web Portal
  
• The tissue microarray data exchange specification
  
• Tissue Array Research Program (TARP) - a collaborative effort between The National Cancer Institute and The National Human Genome Research Institute. The primary objective of TARP is to develop and disseminate Multi-Tumor Tissue Microarray slides and the related technology to the cancer research investigators.
• Tissue Microarray - a very comprehensive page which contains information about tissue array overview, facilities and equipments, tissue array slides, and tissue array analysis tools.
  
• Tissue microarray construction and analysis - protocols provided by NHGRI tissue microarray project
• UCLA Tissue Array Core Facility
• Yale Cancer Center Tissue Microarray Facility
• Yale Tissue Microarray Construction Protocols (pdf)
  

Hardware

• ADVANCED TISSUE ARRAYER ATA 100 - create customized arrays of multiple tissue specimens on a single slide, product of Chemicon International.
• BLISS - automated microscope controlled by a multiprocessor workstation. It has the unique capability to digitize an entire microscope slide at multiple objective magnification levels with an adjustable depth of field and create a distributable virtual microscope slide, the WebSlide; product of Bacus Laboratories Inc.
  
• Discovery-TMA - a high-speed automated optical platform and integrated software system optimized for the acquisition, processing and analysis of images from tissue microarrays; product of Universal Imaging Corp.
  
• Macro Tape-Transfer System - assist sectioning of the tumor array blocks, manufactured by Instrumedics.
• Tissue microarray instrument - Manual and Automatic instrument manufactured by Beecher Instruments to prepare tissue microarray.
• Virtual Microarray Solution - The solution comprises of the ScanScope slide scanner and software for remotely viewing virtual slides that are stored on an image server; product of Aperio Technologies.
  

Software

TMA slides (pre-made)

• Biochain’s Tissue Array - Human, Fetal, Tumor, Alzheimer's disease, Mouse, Rat and Monkey tissue arrays; products of BioChain.
• Clinomics™ Tissue MicroArray systems
  
• Human Cancer Tissue Arrays - 63 tumor tissue spots from 20 patients (each tumor tissue is spotted three times on the slide) and normal tissue spots from three individuals; product of MTR scientific.
• InnoGenex Tissues and Tissue Microarrays - Human Tissue Microarrays, Human Single-Tissue Section Slides, Mouse/Rat Tissue Microarrays, Mouse Single-Tissue Section Slides, Rat Single-Tissue Section Slides; product of InnoGenex.
  
• Multiple Tissue Arrays (MTA) - mouse tissue arrays; product of BD Biosciences Pharmingen.
  
• Stratagene’s Complete View™ tissue array - The Complete View survey array slides represent major organ systems of murine, consisting of approximately 104 cell types mounted in duplicate. The Complete View validation array slides include 12 representative tissues from the survey arrays and are useful to test staining procedures and reagents.
  
• Tissue Arrays - Human tissues, Fetal tissues, Human cancer cell lines and animal tissues arrays; products of SuperBioChips Laboratories.
• Tissue Array/Histo-Array™ - human tissues, cancers, fetal, rat, mouse tissue microarrays; products of Imgenex.
  
• VastArray Tissue Arrays - containing 200 * 600 um core tissues from normal human and mouse organs.
  

Biochip/ Lab-on-a-chip/ Micro Total Analysis System (uTAS)

• Agilent - providing one of the first commercial lab-on-a-chip instruments in the world - Agilent 2100 bioanalyzer for DNA, RNA, proteins and cells analysis.
• Beijing Biochip R&D center - The biggest biochip center in TsingHua University, China
• Caliper - leader in lab-on-a-chip technologies, co-developed Agilent 2100 bioanalyzer.
• Engelhardt Institute of Molecular Biology Russian Academy of Sciences
• Lab-on-a-Chip (Journal)
• Lab-on-a-chip.com- An excellent and comprehensive homepage for everything you can imagine for biochip.
• Lab on a chip network - The Laboratory on a Chip Network (LOCN) brings together the resources of the UK Lab on a Chip Consortium,with those of the Royal  Society of Chemistry and other organisations.
• Micronics -a leader in fluid miniaturization solutions that integrate and automate laboratory processes on a single, disposable, and cost-effective lab chip. The Company is uniquely able to work with complex fluids, like whole blood, and has core capabilities in diffusion-based detection, filtration methods and microcytometry all in a plastic laminate format.

Education

• BIOSTATISTICS 140.688: STATISTICS FOR GENE EXPRESSION SYLLABUS and READING LIST - a course by Prof. Giovanni Parmigiani with step by step reading list on contemporary data analysis methods. Most of the literatures are link to the full text pdf file.
• GeneEd - offers online courses for profit
• Microarrays 201 [preview]
• Mathematical Sciences Research Institute (MSRI) - provides a number of online video seminars on mathematical analysis on genomics, microarray, bioinformatics, proteomics, linkage analysis and genome mapping
• Dynamical Modeling of Complex Biomedical Systems, April 26 - 28, 2001, Washington, D.C.
• Statistics and Microarray Data - by Terry Speed [video]
• Nonlinear Estimation and Classification, March 19 - 29, 2001
• Nonlinear estimation and classification: Challenges from genomics - by Terry Speed [video]
• From bits to information: Theory and applications of learning machines - by Tomaso Poggio [video]
• Computationally intensive statistical methods for microarray based drug discovery - by Katherine Pollard and Mark van der Laan [video]
• Analysis of Transcription Profiling Data Using Generative and Discriminative Methods - by Saira Mian [video]
• Using robust and resistant regression analysis (MM-estimator) to find differentially expressed genes in microarray data - by Alexander Loguinov, Rus Yukhananov, Christopher Vulpe and Saira Mian [video]
• High dimension - low sample size data analysis - by Steve Marron [video]
• MSRI/PMMB Short Course: Mathematical and Computational Challenges in Molecular and  Cell Biology, June 12-23, 2000
• Some Combinatorial and Algorithmic Problems Related to DNA Microarrays - by Richard Karp [video]
• Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling -  by Alter O [video] The original paper was "Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10101-6. [PubMed][pdf][appendix][web supplement]"
• Extracting Regulatory Motifs from Genomes and Microarray data - by Eric Siggia [video]
• Mathematics and Computational Biology of Genome Analysis, June 12-23, 2000
• Making the most of microarray experiments - by Gary A. Churchill [video]
• A model-based expression index from oligonucleotide expression arrays - by Wing Hung Wong [video]
• Computational Methods in Analyzing Gene Expression Data - by Amir Ben-Dor [video]
• Understanding the Genome: Technological and Mathematical Challenges, May 21-23, 1998
• Genes, Chips, and Genomes - by Robert Lipshutz [video]
• Mining Gene Expression Data - by Donna Slonim [video]
• Multivariate Techniques for Biological Data Processing - Excellent introduction and exercises for cluster analysis, principal component analysis (PCA) and multiple regression.
• North Dakota State University Virtual Seminar
• June 11, 2001. Protein and Multicolor Microarrays - by Dr. Robert Fleming-Jones [video]
• SpotFire Genomic Webcast - various online webcast by SpotFire, mainly focus on using their product for array data analysis
• November 1, 2001. Spotfire DecisionSite for Functional Genomics: Getting the most out of Affymetrix Data - by David Nick [video][slide]
• September 25, 2001. Spotfire® DecisionSite for Functional Genomics™ : Benefits of Task Automation in Gene Expression Analysis Software Applications - by David Nick [video][slide]
• May 18, 2001. Protein and Polypeptide Microarrays: Development,  Optimization, and Application to Serum Analysis. - by Dr. Brian B. Haab. [slides]
• April 20, 2001. Affymetrix Data Integration with Spotfire Array Explorer - by Dr. James Flynn [slides]
• March 30, 2001. Using the Distinction Calculation and Portfolio to Create Gene  Lists in Spotfire Array Explorer - by Dr. James Flynn [slides]
• March 16, 2001. Hierarchical Clustering and Heat Maps With  Spotfire Array Explorer - by Dr. James Flynn [slides]
• March 2, 2001. Gene Expression Profiles, Similarity Searches and K-Means Clustering with Spotfire Array Explorer - by Dr. James Flynn [slides]
• February 16, 2001. Quality Control, Scaling and Normalization Across Multiple Microarray Experiments Using Spotfire Array Explorer - by Dr. James Flynn [slides]
• February 2, 2001.  Data Import and Normalization Using Spotfire Array Explorer - by Dr. James Flynn [slides]
• January 16, 2001. Molecular Classification of Cancer - by Dr. Pablo Tamayo [slides]
• Statistics 710 Modeling and Computational Issues in Bioinformatics - The online course notes by Shedden K from University of Michigan. The course covers basic review of modern molecular biology, analysis of Affymetrix GeneChip data, Supervised and Unsupervised learning, PCA, MDS, cluster analysis, classification,  SVM and  Boolean networks.
• Statistics 606 Statistical Computing - The online course notes by Shedden K from University of Michigan. Related topics included Eigenvalue decompostion, singular value decomposition, Bayes models and Markov Chain Monte Carlo.
• Statistics & Genomics Short Course Department of Biostatistics Harvard School of Public Health January 23-25,2002
• The Statistic Homepage - A comprehensive electronic statistic textbook by statsoft
• Univariate statistical methods - A simple univariate statistical methods revision, using some biological related data as examples

Database

Language & Standard

• GeneXML (GeneX Gene Expression Markup Language) - XML developed by National Center for Genome Resources (NCGR).
• GEML (Gene Expression Markup Language) - an Extensible Markup Language (XML)-based tag set, was developed by Rosetta Inpharmatics and others in the GEML community to  provide a standard method of exchanging gene expression data along with the associated gene and experiment annotation.
• MAML (Microarray Markup Language) - facilitate the communication of information about DNA microarray experiment, originally proposed by but no longer supported by Microarray Gene Expression Database (MGED) group. Project development hosted on sourceFORGE.net.
• MAGE-ML (MicroArray and Gene Expression Markup Language) - a language designed to describe and communicate information about microarray based experiments, supported by Microarray Gene Expression Database (MGED) group. Futher informaton from XML cover page.
• MGED Ontology Working Group
  
• MIAME (Minimum Information About a Microarray Experiment) - a standard specifies the minimum information that must be reported about an array based gene expression monitoring experiment in order to ensure the interpretability of the results, as well as potential verification by third parties, proposed by Microarray Gene Expression Database (MGED) group. The publication in Nature Genetics.
• PartisanXML - an XML-based tag set, was developed by Clondiag for Partisan systems. It supports experiment, sample, array information exchange.

Institutes/ Core facilities

• African Centre for Gene Technologies (ACGT) Microarray Facility, South Africa - Providing cDNA and oligo spotting and microarray scanning service to African researchers. Situated in research environment focussing on agricultural and forestry related biotechnologies.
  
• Arabidopsis Functional Genomics Consortium (AFGC) Microarray Services - providing resources for Arabidopsis genomics and microarray study.
• Baylor College of Medicine Micorarray Core Facility - provides Baylor affiliated researchers access to microarray technology
• Duke Center for Genome Technology DNA Microarray Center
  
• EBI microarray informatics - EBI's main effort in microarray is the informatic analysis of expression data. They are also setting up standards for microarray experiments, mailing list and workgroups to facilitate idea sharing.
• Functional genomics at University of California, Irvine
• Genome Consortium for Active Teaching (GCAT) - Bring Functional Genomic Methods into Undergraduate Curriculum Primarily Through Student Research; Use Centralized Chip Reader to Make Microarray Experiments Affordable; Create a Clearing House of Information for Teachers to Use when Teaching Genomics; Create Large Database of Raw Data and Analyzed Results for Pedagogical Use; Develop a Global Network of Teachers Using Functional Genomics in the Undergraduate Curriculum
• HGMP RC Microarray Programme - aimed at developing and disseminating microarray technology to UK academics.
• Microarray Centre at The Ontario Cancer Institute, University Health Network - the centre provides microarray for academic researcher, mainly Canadian.
• Microarray Project - A project initiated by National Human Genome Research Institute which develops protocols, analysis and database software.
• MRC Toxicogenomics
• NASC's Affymetrix Facility - NASC provides a full hybridisation service and transcriptomic analysis service using the Affymetrix GeneChip system. The website has a fully MIAME-supportive description of all the experiments published, together with data mining tools.
  
• Stanford Functional Genomics Facility - The core facility at stanford providing 42,000 elements mouse and human array at US$95, including web based bioinformatic support from the Stanford Microarray Database.
• The Genomics Core Facility, George Washington University Medical Center.
  
• The Microarray Research Group, The Association of Biomolecular Resource Facilities (ABRF) - They performed survey  in 1999-2000 to construct a current portrait of the microarray field that reflects the ongoing dynamic changes in both microarray methodologies and instrumentation and reflects the expanding range of investigators utilizing the technology. You are encouraged to participate in the 2000-2001 survey! You can find the summary of the result here.
• The Sanger Institute Microarray Facility
  
• TIGR Microarray Resource - Microarray links provided by The Institute of Genome Research
• UCLA Microarray Core Facility
• UCSD Array Service
• Whitehead/MIT Genome Center's Molecular Pattern Recognition - developing computational methodologies for the analysis and interpretation of large-scale expressiondatasets generated by DNA micro-array experiments.
• W.M. Keck Foundation Biotechnology Resource Laboratory at Yale - providing various genomics and microarray resources (both affy and DNA)
• Yale Genome Analysis Center - provide full public access to the data and reagents generated from Yale's ongoing functional analysis of the yeast genome.

Labs/ People

• Bolstad, Ben - Dr. Bolstad is involved with Microarray Data analysis in Terry Speed's group 
  
• Botstein, David - Prof. Botstein's group at Stanford University is taking a broad interdisciplinary approach to study the fundamental biology shared by all eukaryotes.
• Brown, Patrick O - Dr. Patrick Brown's group at Stanford University is famous for setting up many standards for microarray experiments and they are now working in many cutting edge researches using microarray technologies.
• Carey, VJ
  
• Cheung, Vivian - Dr. Cheung's lab is focused on developing Direct Identical-by-Descent (IBD) Mapping. Direct IBD Mapping is a DNA microarray-based mapping technique that allows isolation and mapping of DNA fragments shared IBD between individuals.
• Church, George M - Prof Church's group at Harvard University focuses in using quantitative whole genome and proteome measures to guide computational modeling of  regulatory and enzymatic networks in microbial and mammalian cells.
• Churchill, Gary - Dr. Churchill's statistical genetics group at The Jackson Laboratory focused in analysis of data from large scale gene expression assays. There are a few very interesting papers on statistical microarray data analysis in his homepage
• Derisi, Joesph - Dr. Derisi's group at UCSF is using whole genome approaches to tackle problems in yeast molecular biology and human infectious disease.
• Diagnostic microbial microarray projects - A project based in the Department of Biotechnology of the ARC Seibersdorf research GmbH, Seibersdorf, Austria, that aims at developing and applying oligonucleotide microarrays for the high-throughput quantitative detection of microbes.
  
• Dudoit, Sandrine - Dr. Dudoit in the Division of Biostatistics in the School of Public Health at the University of California at Berkeley is interested in the application of statistics to problems in genetics and molecular biology.
  
• Eisen, Michael B - Dr. Eisen's group at Lawrence Berkeley National Lab is using genomics approach to study a variety of biological problems and develop and apply quantitative analyses of DNA microarray data.
• Functional Pathogenomics of Mucosal Immunity -  a large-scale effort to increase the current understanding of how innate immunity to infectious agents operates, and how it may be enhanced to enable the rational development of new and effective strategies for improving human health and animal productivity and welfare. This project will involve the study of both host and pathogen gene expression responses under multiple infection conditions involving a range of bacteria, viruses, and fungi infecting human, bovine, and chicken models.
  
• Gautier, Laurent - Dr. Gautier is a core member of Bioconductor developers
  
• Gentleman, Robert - Dr. Gentleman is interested in statistical computing. A research project started with Ross Ihaka has evolved into the R language. You can find out more about R here . He has also started a new research project (with lots of others) called Bioconductor that is exploring the use of statistical computing (R, of course) in Computational Biology (Bioinformatics, Functional Genomics, Proteomics).
• Gentry, Jeff - Jeff is a developer for the Bioconductor project, which provides open source software for bioinformatics.
• Irizarry, Rafael A. - Dr. Irizarry is interested in 1) The development of software and methods for pre-processing of microarray data and 2) applications of Nonparametric Statistics and Time Series Analysis in the biomedical sciences.
  
• Iyer, Vishy- Dr. Iyer's group at University Texas at Austin is using microarray for mapping the genome-wide physical interactions of transcription factors with their chromosomal targets in yeast and studying transcriptional control mechanisms in cellular proliferation and cancer biology.
• Kim, Stuart - Dr. Stuart Kim group at  Stanford University is interested profiling gene expression patterns in  C. elegans with DNA microarrays.
• Laboratory for the statistical analysis of microarray data - A center for statistical analysis of data arising from DNA microarrays. This lab is sponsored by the Department of Health Research & Policy and the Department of Statistics, Stanford University.
• Liu, Chih Long -  Chih Long Liu is currently a Stanford alumnus ('01, Biological Sciences) and a Harvard graduate student in the BBS PhD program. He is a former Brown Lab member (Biochemistry Department) and initially joined the lab in the summer of 1998 with the development of the cy dye repurification protocol.
• Molecular Statistics and Bioinformatics Section, Biometric Research Branch, NCI - to develop statistical, mathematical and computational methodology for the analysis of genome and gene expression data in order to identify cancer associated genes, elucidate their functions, determine the steps of tumor development, identify molecular targets and develop genome based approaches to the prevention, detection, diagnosis and treatment of cancer.
• Robinson, Alan - Dr. Robinson is the team leader of industry programme at EMBL-EBI, focus in developing new and novel techniques to understand and visualise data with application to problems within the bioinformatics field.
• Schena, Mark - Dr. Schena is the editor for the first 2 microarray books and is the visiting scholar of Telechem arrayit.com
• Smyth, Gordon K - Dr. Smyth is interested in bioinformatics and statistical modelling and computing.
• Speed, Terry - Prof. Speed's microarray data analysis group studies statistical approaches for dealing with different problems arising in the analysis of microarray data. There are several very interesting papers on statistical microarray data analysis in his homepage. They also write a very useful R-package - Statistical Microarray Analysis (SMA)
• Staudt, Louis M - Dr. Staudt group at NCI used microarray to view the gene expression profiles of distinct stages of lymphoid development and compare these to the gene expression profiles of human lymphoid malignancies and aimed to develop new molecular classifications of these cancers.
• Storey, John - Dr. Storey is interested in developing statistical methods useful in understanding data generated from DNA microarrays, large scale genotyping, and genome sequencing.
• Tibshirani, Rob - Prof. Tibshirani from Department of Statistics, Stanford University is the writer of Significance analysis of microarrays (SAM)
• Ward, Sam  - Prof. Ward's team at University of Arizona is using DNA microarray technology to identify genes controlling spermatogenesis
• Weinstein, John N - Prof. Weinstein team at NCI is using genomics and bioinformatics tools to better understand the pharmacology of cancer ells and to find new agents for treatment of cancer.
• White, Kevin  - Dr. White's group at Yale University is using microarray for study development and evolution, using drosophila as a vehicle.
• Yang, Yee Hwa - Dr. Yang's research has centered on the development of statistical methodology and software for the design and analysis of gene-expression data from microarrays.
  

Conference

• Annual Ontario Microarray Network Technology Symposium - 2003-3rd,2001-2nd;
• CAMDA: Critical Assessment of Microarray Data Analysis - 2003 [papers & presentation slides]; 2002 [papers & presentation slides];