Expression profiling using a hexamer-based universal microarray.
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.
Roth
Matthew E
ME
Agilix Corporation, 2 Church Street South, New Haven, Connecticut 06519, USA.
Feng
Li
L
McConnell
Kevin J
KJ
Schaffer
Paul J
PJ
Guerra
Cesar E
CE
Affourtit
Jason P
JP
Piper
Kevin R
KR
Guccione
Lorri
L
Hariharan
Jayashree
J
Ford
Maura J
MJ
Powell
Stephen W
SW
Krishnaswamy
Harish
H
Lane
Jennifer
J
Guccione
Lisa
L
Intrieri
Gino
G
Merkel
Jane S
JS
Perbost
Clotilde
C
Valerio
Anthony
A
Zolla
Brenda
B
Graham
Carol D
CD
Hnath
Jonathan
J
Michaelson
Chris
C
Wang
Rixin
R
Ying
Baoge
B
Halling
Conrad
C
Parman
Craig E
CE
Raha
Debasish
D
Orr
Brent
B
Jedrzkiewicz
Barbara
B
Liao
Ji
J
Tevelev
Anton
A
Mattessich
Martin J
MJ
Kranz
David M
DM
Lacey
Michelle
M
Kaufman
Joseph C
JC
Kim
Junhyong
J
Latimer
Darin R
DR
Lizardi
Paul M
PM
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
D020413:3' Untranslated Regions; D018076:DNA, Complementary; D012333:RNA, Messenger; D004262:DNA Restriction Enzymes; D005690:Galactose