title: Expression profiling using a hexamer-based universal microarray.
abstract: We describe a transcriptional analysis platform consisting of a universal micro-array system (UMAS) combined with an enzymatic manipulation step that is capable of generating expression profiles from any organism without requiring a priori species-specific knowledge of transcript sequences. The transcriptome is converted to cDNA and processed with restriction endonucleases to generate low-complexity pools (approximately 80-120) of equal length DNA fragments. The resulting material is amplified and detected with the UMAS system, comprising all possible 4,096 (4(6)) DNA hexamers. Ligation to the arrays yields thousands of 14-mer sequence tags. The compendium of signals from all pools in the array-of-universal arrays comprises a full-transcriptome expression profile. The technology was validated by analysis of the galactose response of Saccharomyces cerevisiae, and the resulting profiles showed excellent agreement with the literature and real-time PCR assays. The technology was also used to demonstrate expression profiling from a hybrid organism in a proof-of-concept experiment where a T-cell receptor gene was expressed in yeast.
authors.affiliation: Agilix Corporation, 2 Church Street South, New Haven, Connecticut 06519, USA.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Roth
authors.forename: Li
authors.initials: L
authors.lastname: Feng
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: McConnell
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Schaffer
authors.forename: Cesar E
authors.initials: CE
authors.lastname: Guerra
authors.forename: Jason P
authors.initials: JP
authors.lastname: Affourtit
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Piper
authors.forename: Lorri
authors.initials: L
authors.lastname: Guccione
authors.forename: Jayashree
authors.initials: J
authors.lastname: Hariharan
authors.forename: Maura J
authors.initials: MJ
authors.lastname: Ford
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Powell
authors.forename: Harish
authors.initials: H
authors.lastname: Krishnaswamy
authors.forename: Jennifer
authors.initials: J
authors.lastname: Lane
authors.forename: Lisa
authors.initials: L
authors.lastname: Guccione
authors.forename: Gino
authors.initials: G
authors.lastname: Intrieri
authors.forename: Jane S
authors.initials: JS
authors.lastname: Merkel
authors.forename: Clotilde
authors.initials: C
authors.lastname: Perbost
authors.forename: Anthony
authors.initials: A
authors.lastname: Valerio
authors.forename: Brenda
authors.initials: B
authors.lastname: Zolla
authors.forename: Carol D
authors.initials: CD
authors.lastname: Graham
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hnath
authors.forename: Chris
authors.initials: C
authors.lastname: Michaelson
authors.forename: Rixin
authors.initials: R
authors.lastname: Wang
authors.forename: Baoge
authors.initials: B
authors.lastname: Ying
authors.forename: Conrad
authors.initials: C
authors.lastname: Halling
authors.forename: Craig E
authors.initials: CE
authors.lastname: Parman
authors.forename: Debasish
authors.initials: D
authors.lastname: Raha
authors.forename: Brent
authors.initials: B
authors.lastname: Orr
authors.forename: Barbara
authors.initials: B
authors.lastname: Jedrzkiewicz
authors.forename: Ji
authors.initials: J
authors.lastname: Liao
authors.forename: Anton
authors.initials: A
authors.lastname: Tevelev
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Mattessich
authors.forename: David M
authors.initials: DM
authors.lastname: Kranz
authors.forename: Michelle
authors.initials: M
authors.lastname: Lacey
authors.forename: Joseph C
authors.initials: JC
authors.lastname: Kaufman
authors.forename: Junhyong
authors.initials: J
authors.lastname: Kim
authors.forename: Darin R
authors.initials: DR
authors.lastname: Latimer
authors.forename: Paul M
authors.initials: PM
authors.lastname: Lizardi
mesh_terms: D020413:3' Untranslated Regions; D000465:Algorithms; D000818:Animals; D053938:DNA Fragmentation; D004262:DNA Restriction Enzymes / Q000378:metabolism; D018076:DNA, Complementary / Q000378:metabolism; D005690:Galactose / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D051379:Mice; D008957:Models, Genetic; D018482:Muscle, Skeletal / Q000378:metabolism; D009132:Muscles / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013601:T-Lymphocytes / Q000378:metabolism; D019076:Transgenes
chemical_list: D020413:3' Untranslated Regions; D018076:DNA, Complementary; D012333:RNA, Messenger; D004262:DNA Restriction Enzymes; D005690:Galactose