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In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part 3


ABSTRACT: E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples at various input levels. A "full-scale" reference was prepared using the standard input level of 6.0 ug total RNA, and one round of amplification was performed with 250 ng and 50 ng total RNA inputs. For 10 ng and 2 ng inputs, two rounds of amplification were used. Targets were compared on a microarray platform designed for this test using a "dye-swapped" experimental design, and sets of significantly differential genes were compared to the full scale reference's list to determine specificity and sensitivity in terms of detection of significant expression differences. Keywords: dye swap design,quality control testing design E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples at various input levels. A "full-scale" reference was prepared using the standard input level of 6.0 ug total RNA, and one round of amplification was performed with 250 ng and 50 ng total RNA inputs. For 10 ng and 2 ng inputs, two rounds of amplification were used. Targets were compared on a microarray platform designed for this test using a "dye-swapped" experimental design, and sets of significantly differential genes were compared to the full scale reference's list to determine specificity and sensitivity in terms of detection of significant expression differences.

ORGANISM(S): Mus musculus

SUBMITTER: Kazuhiro Aiba 

PROVIDER: E-GEOD-3507 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Carter Mark G MG   Hamatani Toshio T   Sharov Alexei A AA   Carmack Condie E CE   Qian Yong Y   Aiba Kazuhiro K   Ko Naomi T NT   Dudekula Dawood B DB   Brzoska Pius M PM   Hwang S Stuart SS   Ko Minoru S H MS  

Genome research 20030501 5


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 t  ...[more]

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