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

Mark G. Carter, Toshio Hamatani, Alexei A. Sharov, Condie E. Carmack, Yong Qian, Kazuhiro Aiba, Naomi T. Ko, Dawood B. Dudekula, Pius M. Brzoska, S. Stuart Hwang, Minoru Ko

Research output: Contribution to journalArticle

91 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1011-1021
Number of pages11
JournalGenome Research
Volume13
Issue number5
DOIs
Publication statusPublished - 2003 May 1
Externally publishedYes

Fingerprint

Stem Cells
RNA
Stem Cell Research
Embryology
Oligonucleotide Probes
Gene Library
Genes
Research Design
Embryonic Structures
Complementary DNA
Clone Cells
Research Personnel
Technology

ASJC Scopus subject areas

  • Genetics

Cite this

In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. / Carter, Mark G.; 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.

In: Genome Research, Vol. 13, No. 5, 01.05.2003, p. 1011-1021.

Research output: Contribution to journalArticle

Carter, MG, Hamatani, T, Sharov, AA, Carmack, CE, Qian, Y, Aiba, K, Ko, NT, Dudekula, DB, Brzoska, PM, Hwang, SS & Ko, M 2003, 'In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling', Genome Research, vol. 13, no. 5, pp. 1011-1021. https://doi.org/10.1101/gr.878903
Carter, Mark G. ; 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. / In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. In: Genome Research. 2003 ; Vol. 13, No. 5. pp. 1011-1021.
@article{f81c586f143b495a891f8ec6f1608171,
title = "In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling",
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.",
author = "Carter, {Mark G.} and Toshio Hamatani and Sharov, {Alexei A.} and Carmack, {Condie E.} and Yong Qian and Kazuhiro Aiba and Ko, {Naomi T.} and Dudekula, {Dawood B.} and Brzoska, {Pius M.} and Hwang, {S. Stuart} and Minoru Ko",
year = "2003",
month = "5",
day = "1",
doi = "10.1101/gr.878903",
language = "English",
volume = "13",
pages = "1011--1021",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "5",

}

TY - JOUR

T1 - In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling

AU - Carter, Mark G.

AU - Hamatani, Toshio

AU - Sharov, Alexei A.

AU - Carmack, Condie E.

AU - Qian, Yong

AU - Aiba, Kazuhiro

AU - Ko, Naomi T.

AU - Dudekula, Dawood B.

AU - Brzoska, Pius M.

AU - Hwang, S. Stuart

AU - Ko, Minoru

PY - 2003/5/1

Y1 - 2003/5/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=0038781861&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0038781861&partnerID=8YFLogxK

U2 - 10.1101/gr.878903

DO - 10.1101/gr.878903

M3 - Article

VL - 13

SP - 1011

EP - 1021

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 5

ER -