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Protocols

• A Concise Guide to cDNA Microarray Analysis (The Institute for Genomic Research)
  Standard protocol including Array Fabrication, Probe Preparation and Hybridization, and Data Collection, Normalization and Analysis. This is a 27-page PDF file.
  http://pga.tigr.org/PDF/BiotechniquesCookbook_II.p...
  Added: Fri Oct 04 2002, Hits: 2722, Reviews: 0  Write review  
• MicroArray Protocol (HuGEIndex.org)
  Basic Steps of microArray experiments
  • Total RNA Isolation from cultured cells.
  • DNase Treatment of Total RNA
  • Making the single strand cDNA probe.
  • Automated Slide Processor (ASP) Version for hybridization.
  • Washing microarrays in ASP.
  • Processing of Array slide
  • Pre-hybridization of the processed slides (NON-Automated version).
  • Hybridization of Cy3 + Cy5 probe to glass array (NON-Automated version).
  • Preparation of Dendrimer Cy3 and Cy5.
  • Washing unbound probe from glass array (NON-Automated version).
  • Hybridization of Dendrimers (Cy3 and Cy5) to Array (NON-Automated version).
  • Washing unbound dendrimer from glass array(NON-Automated version).
  
  http://132.183.243.138/hio/microarray/microprocedu...
  Added: Tue Sep 24 2002, Hits: 3983, Reviews: 1 Read reviews  Write review  
• Microarray Protocol (National Human Genome Research Institute)
  This set of protocols is intended to serve as a basic introduction to making and using cDNA microarrays. There are three fundamental types of operations required in a cDNA microarray experiment. The first operation, BASIC PROTOCOL 1, cDNA AMPLIFICATION AND PRINTING, deals with making the cDNA microarray itself. BASIC PROTOCOL 2, RNA EXTRACTION AND LABELING, RNA is extracted from the cell samples to be examined, purified, and used as the substrate for reverse transcription in the presence of fluor-derivatized nucleotides. BASIC PROTOCOL 3, HYBRIDIZATION AND DATA EXTRACTION, covers the steps in which fluor-labeled cDNAs hybridize to their complements on the microarray, and the resulting localized concentrations of fluorescent molecules are detected and quantitated.
  http://research.nhgri.nih.gov/microarray/protocols...
  Added: Wed Sep 25 2002, Hits: 2981, Reviews: 0  Write review   Cached
• cDNA Microarray Protocol (National Human Genome Research Institute, NHGRI)
  There are three fundamental types of operations required in a cDNA microarray experiment. 1, cDNA AMPLIFICATION AND PRINTING, deals with making the cDNA microarray itself. It is necessary to collect an inventory of cDNA bacterial clones that represent the genes whose message abundance you wish to survey. 2, RNA EXTRACTION AND LABELING, RNA is extracted from the cell samples to be examined, purified, and used as the substrate for reverse transcription in the presence of fluor-derivatized nucleotides. 3, HYBRIDIZATION AND DATA EXTRACTION, covers the steps in which fluor-labeled cDNAs hybridize to their complements on the microarray, and the resulting localized concentrations of fluorescent molecules are detected and quantitated.
  http://research.nhgri.nih.gov/microarray/protocols...
  Added: Tue May 14 2002, Hits: 1820, Reviews: 0  Write review   Cached
• Cyanine Dye HPLC Purification (Pat Brown Lab, Department of Biochemistry and the Howard Hughes Medical Institute)
  Sep-Pak and HPLC purification protocol for Cy dyes (un)incorporated with dNTP
  http://cmgm.stanford.edu/pbrown/mguide/hplc.html
  Added: Tue May 14 2002, Hits: 775, Reviews: 0  Write review   Cached
• DNA Microarray Protocols (DeRisi Lab, Dept. of Biochemistry & Biophysics, Univ. of California at San Francisco)
  Very detailed protocols for microarray experiments starting from preparing nuclear acid from a variety of sources, labeling, and more...
  http://www.microarrays.org/protocols.html
  Added: Tue May 14 2002, Hits: 519, Reviews: 0  Write review   Cached
• Making a scanning array (Practical Approach Online, Oxford University Press)
  In situ synthesis of oligonucleotides on a solid substrate
  http://www.oup.co.uk/pdf/pas/6-5-3.pdf
  Added: Tue Sep 24 2002, Hits: 745, Reviews: 0  Write review  
• Microarray Development Protocols (Vodkin Laboratory, University of Illinois)
  Protocols used for a whole microarray experiment including: Preparation of DNA for microarrays / Electrophoresis of PCR products /Purification of PCR products with Sephadex / Preparing poly-L-lysine coated slides / Postprint slide treatments / Postprint blocking of amine slides Postprint blocking of aldehyde slides / Reverse transcriptase labeling with Cy3/Cy5 / Staining of total DNA on slides /Microarray construction /Laser scanning Spot quantitation/ Statistics of expression Sample tracking /Controls used in the microarrays
  http://soybeangenomics.cropsci.uiuc.edu/protocols/...
  Added: Mon Aug 26 2002, Hits: 1182, Reviews: 0  Write review   Cached
• Microarray Protocol (KRL)
  A set of protocols for microarray experiments: Reagents & Equipments/Labelling/Purification/Hybridisation/Washing
  http://www.rbhrfcrc.qimr.edu.au/kidney/Pages/Micro...
  Added: Tue Sep 24 2002, Hits: 1101, Reviews: 0  Write review   Cached
• Modified Eberwine ("antisense") RNA Amplification Protocol (Pat Brown Lab, Department of Biochemistry and the Howard Hughes Medical Institute)
  http://cmgm.stanford.edu/pbrown/protocols/ampproto...
  Added: Tue May 14 2002, Hits: 153, Reviews: 0  Write review   Cached
• Stripping an array (Practical Approach Online, Oxford University Press)
  Stripping an anrray for reuse
  http://www.oup.co.uk/pdf/pas/6-5-10.pdf
  Added: Mon Aug 26 2002, Hits: 857, Reviews: 0  Write review  
• TIGR Microarray Protocols and Standard Operating Procedures (The Institute for Genomic Research)
  Template Preparation / PCR Purification and Storage / Printing in DMSO / Amino-allyl Labeling / Labeled Probe Hybridization
  http://www.tigr.org/tdb/microarray/protocolsTIGR.s...
  Added: Fri Oct 04 2002, Hits: 1038, Reviews: 0  Write review   Cached