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PMID: 12727912 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling.

Genome research ·Vol. 13 ·No. 5 ·2003-05-00 ·Pages 1011-21

Carter MG, Hamatani T, Sharov AA, Carmack CE, Qian Y, Aiba K, Ko NT, Dudekula DB, Brzoska PM, Hwang SS, Ko MS

Abstract

Applications of microarray technologies to mouse embryology/genetics have been limited, due to the nonavailability of microarrays containing large numbers of embryonic genes and the gap between microgram quantities of RNA required by typical microarray methods and the miniscule amounts of tissue available to researchers. To overcome these problems, we have developed a microarray platform containing in situ-synthesized 60-mer oligonucleotide probes representing approximately 22,000 unique mouse transcripts, assembled primarily from sequences of stem cell and embryo cDNA libraries. We have optimized RNA labeling protocols and experimental designs to use as little as 2 ng total RNA reliably and reproducibly. At least 98% of the probes contained in the microarray correspond to clones in our publicly available collections, making cDNAs readily available for further experimentation on genes of interest. These characteristics, combined with the ability to profile very small samples, make this system a resource for stem cell and embryogenomics research.

MeSH Terms
Animals Embryo, Mammalian/chemistry,metabolism Female Gene Expression Profiling/methods,statistics & numerical data Gene Expression Regulation, Developmental/genetics In Situ Hybridization/methods,statistics & numerical data Mice Mice, Inbred C57BL Multigene Family/genetics Oligonucleotide Array Sequence Analysis/methods,statistics & numerical data Oligonucleotides/biosynthesis Placenta/chemistry,metabolism Polymerase Chain Reaction/methods,statistics & numerical data RNA/genetics Sensitivity and Specificity Stem Cells/chemistry,metabolism
Chemicals
Oligonucleotides RNA
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Carter Mark G
Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging (NIA), National Institutes of Health, Baltimore, Maryland 20892, USA.
Hamatani Toshio
Sharov Alexei A
Carmack Condie E
Qian Yong
Aiba Kazuhiro
Ko Naomi T
Dudekula Dawood B
Brzoska Pius M
Hwang S Stuart
Ko Minoru S H
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.878903
Published
2003-05-00
Pages
1011-21
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC430900
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.878903 PMC Full Text View journal details
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