title: An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes.
abstract: Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148,993 and 121,703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25,342 human and 24,109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity score; (ii) the number of expressed sequence tags matching each probe; (iii) the distance to the 3' end of the target mRNA. Scores were also used to compare in silico the two microarrays with commercial microarrays. The sets described here, called RNG/MRC collections, appear at least as specific and sensitive as those from the commercial platforms. The RNG/MRC collections have now been used by an Anglo-French consortium to distribute more than 3500 microarrays to the academic community. Ad hoc identification of tissue-specific transcripts and a approximately 80% correlation with hybridizations performed on Affymetrix GeneChiptrade mark suggest that the RNG/MRC microarrays perform well. This work provides a comprehensive open resource for investigators working on human and mouse transcriptomes, as well as a generic method to generate new microarray collections in other organisms. All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE.
authors.affiliation: CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, UMR6097, 660, route des Lucioles, F-06560 Sophia Antipolis, France.
authors.forename: Kévin
authors.initials: K
authors.lastname: Le Brigand
authors.forename: Roslin
authors.initials: R
authors.lastname: Russell
authors.forename: Chimène
authors.initials: C
authors.lastname: Moreilhon
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Rouillard
authors.forename: Bernard
authors.initials: B
authors.lastname: Jost
authors.forename: Franck
authors.initials: F
authors.lastname: Amiot
authors.forename: Virginie
authors.initials: V
authors.lastname: Magnone
authors.forename: Christine
authors.initials: C
authors.lastname: Bole-Feysot
authors.forename: Philippe
authors.initials: P
authors.lastname: Rostagno
authors.forename: Virginie
authors.initials: V
authors.lastname: Virolle
authors.forename: Virginie
authors.initials: V
authors.lastname: Defamie
authors.forename: Philippe
authors.initials: P
authors.lastname: Dessen
authors.forename: Gary
authors.initials: G
authors.lastname: Williams
authors.forename: Paul
authors.initials: P
authors.lastname: Lyons
authors.forename: Géraldine
authors.initials: G
authors.lastname: Rios
authors.forename: Bernard
authors.initials: B
authors.lastname: Mari
authors.forename: Erdogan
authors.initials: E
authors.lastname: Gulari
authors.forename: Philippe
authors.initials: P
authors.lastname: Kastner
authors.forename: Xavier
authors.initials: X
authors.lastname: Gidrol
authors.forename: Tom C
authors.initials: TC
authors.lastname: Freeman
authors.forename: Pascal
authors.initials: P
authors.lastname: Barbry
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D051379:Mice / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes / Q000737:chemistry*; D014158:Transcription, Genetic
chemical_list: D015345:Oligonucleotide Probes