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In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part1

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 and compared on a novel microarray design to validate the system. A "dye-swapped" experimental design was used to assess the accuracy and precision of the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection. Keywords: dye swap design,quality control testing design

ORGANISM(S): Mus musculus

PROVIDER: GSE3516 | GEO | 2005/10/28

SECONDARY ACCESSION(S): PRJNA93563

REPOSITORIES: GEO

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In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part1

Project description: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 and compared on a novel microarray design to validate the system. A "dye-swapped" experimental design was used to assess the accuracy and precision of the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection. 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 and compared on a novel microarray design to validate the system. A "dye-swapped" experimental design was used to assess the accuracy and precision of the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.

2010-06-30 | E-GEOD-3516 | biostudies-arrayexpress

In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part2

Project description: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 and compared on a novel microarray design to validate the system. A "self-versus-self" experimental design was used to assess the false-positive rates in the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection. Keywords: self vs self design

2005-10-28 | GSE3513 | GEO

In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part2

Project description: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 and compared on a novel microarray design to validate the system. A "self-versus-self" experimental design was used to assess the false-positive rates in the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection. Keywords: self vs self 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 and compared on a novel microarray design to validate the system. A "self-versus-self" experimental design was used to assess the false-positive rates in the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.

2010-06-30 | E-GEOD-3513 | biostudies-arrayexpress

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

2005-10-28 | GSE3507 | GEO

Transcription profiling of E12.5 mouse whole embryos and placentas pooled within 3 litters to validate a new array

Project description: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 and compared on a novel microarray design to validate the system. A "dye-swapped" experimental design was used to assess the accuracy and precision of the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.

2005-01-01 | E-MNIA-69 | biostudies-arrayexpress

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

Project description: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.

2010-06-30 | E-GEOD-3507 | biostudies-arrayexpress

Transcription profiling of E12.5 mouse whole embryos and placentas pooled within 3 litters and used to valdiate a new array

Project description: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 and compared on a novel microarray design to validate the system. A "self-versus-self" experimental design was used to assess the false-positive rates in the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.

2005-01-01 | E-MNIA-68 | biostudies-arrayexpress

Runx1 (Aml1) knockdown in AMkL Meg-01 cells

Project description:Transcriptional profiling of the effect of shRNA silencing of Runx1 in human AMkL Meg-01 cells. RNA samples obtained from two independent colonies were compared to RNAs from negative control transductions in a two-color design. A total of four microarrays were completed, with a dye-swapped pair performed for each colony.

2009-08-01 | GSE17311 | GEO

Time course response of Synechocystis PCC 6803 to dehydration/desiccation

Project description:The responses of the transcriptome were monitored in Synechocysis PCC 6803 during a linear rate of evaporation of the culture to dryness (desiccation). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: Dehydration, stress response, time course, transcription, cyanobacteria

2006-09-04 | GSE4604 | GEO

Synechocystis PCC6803 time course responses to cadmium (CdSO4, 50 microM, 300 min.

Project description:The transcriptome approach was used to characterize the of the global change in Synechocystis gene expression in response to continuous exposure to cadmium (50 microM). Total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: stress responses

2005-12-07 | GSE3718 | GEO

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