2010 Lab 8

Microarray Laboratory

Microarray Slide

Introduction

The first half of this laboratory will be a visit to the UNSW The Ramaciotti Centre for Gene Function Analysis. This follows on from the theoretical lab last week discussing methods of analysis, you will have the opportunity to see the practical aspects of the new methods of cell analysis. Have a look through the centre's website before you visit and the other links to information on microarrays.

Links

Microarray technology

• The Ramaciotti Centre for Gene Function Analysis
  • Homepage
  • About the centre
  • Services
  • Affymetrix
• NCBI Microarray Factsheet
• Stanford School of Medicine Microarray Database
• EMBL Microarray Informatics at the EBI
• Commercial
  • Affymetrix
• Education
  • Davidson College DNA Microarray Methodology - Flash Animation

References

Textbooks

Essential Cell Biology

• Essential Cell Biology Chapter

Molecular Biology of the Cell

Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter New York and London: Garland Science; c2002

• Methods - Studying Gene Expression and Function
• Microarrays Monitor the Expression of Thousands of Genes at Once
• Figure 8-62. Using DNA microarrays to monitor the expression of thousands of genes simultaneously

Molecular Cell Biology

Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E. New York: W. H. Freeman & Co.; c1999

• 7.8. DNA Microarrays: Analyzing Genome-Wide Expression

Madame Curie Bioscience Database

Chapters taken from the Madame Curie Bioscience Database (formerly, Eurekah Bioscience Database) Eurekah.com and Landes Bioscience and Springer Science+Business Media; c2009

• The Use of Microarray Analysis to Molecularly Characterize Muscle Development
• Analysis of microarray data to discover new tumor classification and to build gene predictors for cancer diagnosis
• Identification of Biologically Relevant Networks

Search Online Textbooks

• "microarray" Bookshelf
• "DNA sequencing" sequencing Bookshelf

PubMed

• PubMed is a service of the U.S. National Library of Medicine that includes over 18 million citations from MEDLINE and other life science journals for biomedical articles back to 1948. PubMed includes links to full text articles and other related resources. PubMed

• PubMed Central (PMC) is a free digital archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health (NIH) in the National Library of Medicine (NLM) allowing all users free access to the material in PubMed Central. PMC

• Online Mendelian Inheritance in Man (OMIM) is a comprehensive compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM

• Entrez is the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others Entrez

Search Pubmed

• "microarray" Entrez all databases
• "DNA sequencing" Entrez all databases
• "gene analysis" Entrez all databases

Reviews

• Microarray-based genomic DNA profiling technologies in clinical molecular diagnostics. Shen Y, Wu BL. Clin Chem. 2009 Apr;55(4):659-69. Epub 2009 Feb 20. Review PMID: 19233918
• Peptide microarrays for serum antibody diagnostics. Andresen H, Bier FF. Methods Mol Biol. 2009;509:123-34. Review. PMID: 19212718
• Microarrays under the microscope. Wildsmith SE, Elcock FJ. Mol Pathol. 2001 Feb;54(1):8-16. Review. PMID: 11212888
• Large-scale gene expression data analysis: a new challenge to computational biologists. Zhang MQ. Genome Res. 1999 Aug;9(8):681-8. Review. Erratum in: Genome Res 1999 Nov;9(11):1156. PMID: 10447504
• Microarrays: biotechnology's discovery platform for functional genomics. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW. Trends Biotechnol. 1998 Jul;16(7):301-6. Review. PMID: 9675914

2010 Course Content

Lectures: Cell Biology Introduction | Cells Eukaryotes and Prokaryotes | Cell Membranes and Compartments | Cell Nucleus | Cell Export - Exocytosis | Cell Import - Endocytosis | Cell Mitochondria | Cell Junctions | Cytoskeleton Introduction | Cytoskeleton 1 Intermediate Filaments | Cytoskeleton 2 Microtubules | Cytoskeleton 3 Microfilaments | Extracellular Matrix 1 | Extracellular Matrix 2 | Cell Cycle | Cell Division | Cell Death 1 | Cell Death 2 | Signal 1 | Signal 2 | Stem Cells 1 | Stem Cells 2 | Development | Revision

Laboratories: Introduction to Lab | Microscopy Methods | Preparation/Fixation | Immunochemistry | Cell Knockout Methods | Cytoskeleton Exercise | Confocal Microscopy | Microarray Visit | Tissue Culture 1 | Tissue Culture 2 | Stem Cells Lab | Stem Cells Analysis

Dr Mark Hill 2013, UNSW Cell Biology - UNSW CRICOS Provider Code No. 00098G