An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes.
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.
Le Brigand
Kévin
K
CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, UMR6097, 660, route des Lucioles, F-06560 Sophia Antipolis, France.
Russell
Roslin
R
Moreilhon
Chimène
C
Rouillard
Jean-Marie
JM
Jost
Bernard
B
Amiot
Franck
F
Magnone
Virginie
V
Bole-Feysot
Christine
C
Rostagno
Philippe
P
Virolle
Virginie
V
Defamie
Virginie
V
Dessen
Philippe
P
Williams
Gary
G
Lyons
Paul
P
Rios
Géraldine
G
Mari
Bernard
B
Gulari
Erdogan
E
Kastner
Philippe
P
Gidrol
Xavier
X
Freeman
Tom C
TC
Barbry
Pascal
P
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
D015345:Oligonucleotide Probes