MIAME/Protocol

Useful Resources

Data Management/Publication > MIAME/Protocol (21)

	Northwestern University, Center for Genetic Medicine (Microarray Core Facility) Protocols for labeling and hybridization. http://www.cgm.northwestern.edu/
	Ensembl Genome Browser Produces and maintains automatic annotation on selected eukaryotic genomes, concentrating on vertebrate genomes. http://www.ensembl.org/
	FlyChip: The UK Drosophila Microarray Facility Functional genomics for Drosophila http://www.flychip.org.uk/links/curation.php
	Fox Chase Cancer Center Protocol in the following areas: clone PCR amplification, microarray spotting procedure, indirect cDNA probe labeling, and microarray quality control and hybridization. http://www.fccc.edu/research/labs/microarray/protocols.html
	GenBank GenBank is a database of nucleotide sequences. http://www.ncbi.nlm.nih.gov/genbank
	GeneAnnot GeneAnnot provides an annotation of Affymetrix probe-sets. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match. http://genecards.weizmann.ac.il/geneannot/
	GeneCards The database offers concise information about human genes (and their mouse homologs), with a focus on their cellular functions and medical aspects. http://www.genecards.org/index.shtml
	HCNetDat Annotation Database A gene annotation database for Affymetrix GeneChips and spotted cDNA arrays http://www.stjuderesearch.org/hcnetdat/
	HomoloGene A gene homology tool that compares nucleotide sequences between pairs of organisms, providing automated detection of homologs among the annotated genes of several eukaryotic genomes. Using HomoloGene, annotation can be combined and compared across organisms. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
	MaxdLoad2 and maxdBrowse Standards-compliant tools for microarray experimental annotation, data management and dissemination. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1298287
	Microarray Databases and MIAME This presentation provides a review of microarray data/databases and an explanation of what MIAME is. http://titan.biotec.uiuc.edu/cs491jh/slides/cs491jh-Yong.ppt
	Microarray Gene Expression Data Society The homepage for MIAME ("Minimum information about a microarray experiment" needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.). It provides a checklist to allow researchers to produce MIAME compliant experiment. http://www.mged.org/
	Microarray World This page consists of an organized, extensive set of links to facilitate access to microarray printing, RNA isolation, probe labeling and scanning techniques. http://microarrayworld.com/ProtocolPage.html
	Mount Sinai School of Medicine (Microarray Shared Research Facility) GeneChip system protocols http://www.mssm.edu/
	Pangloss Wisdom Protocol include mRNA purification, slide hybridization, and the post processing of arrays. http://www.pangloss.com/
	Partners Research Cores- DNA Microarray Core The Core has developed a comprehensive program of the microarray process to give the requisite experience to analyze and interpret microarray data. They use spotted DNA microarrays exclusively, and currently offer 34k Human and 20k Mouse arrays. http://www.partners.org/researchcores/microarray/microarray_seed_MGH.asp
	Stanford University Center for Molecular and Genetic Medicine Protocols described include post-processing of oligo arrays, hybridization, and DNA and slide preparation. http://cmgm.stanford.edu/pbrown/protocols/
	Stowers Institute for Medical Research Protocols described are: post-processing of DNA microarrays printed with long oligos (70mers), flourescent probe preparation by amino-allyl reverse transcription, total RNA prep from yeast, zymo columns for probe cleanup, purification of mRNA with OliogoTex beads, examination of RNA with Agilent BioAnalyzer. http://research.stowers-institute.org/
	The Paterson Institute for Cancer Research Documents to help in the design of a MIAME compliant experiment with an Affymetrix system. http://bioinf.picr.man.ac.uk/mbcf/miame_ma.jsp
	University of Arizona Protocols associated with botany arraying. http://latin.arizona.edu/

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