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| Status |
Public on Oct 28, 2005 |
| Title |
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (22k Linearity) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation. These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene). Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta.
Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design
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| Overall design |
E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation. These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene). Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta.
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| Contributor(s) |
Carter MG, Sharov AA, VanBuren V, Dudekula DB, Carmack CE, Nelson C, Ko MS |
| Citation(s) |
15998450 |
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| Submission date |
Oct 25, 2005 |
| Last update date |
Jan 17, 2013 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
kom@mail.nih.gov
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| Phone |
410-558-8359
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| Organization name |
NIH
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| Department |
National Institute on Aging
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| Lab |
Lab of Genetics
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| Street address |
251 Bayview Blvd, Suite 100, 10C
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| Platforms (1) |
| GPL2549 |
NIA Mouse 22K Microarray v2.0 (Development 60-mer Oligo) |
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| Samples (10)
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| GSM80045 |
E12.5 Embryos1, 5 pooled(16012165010011) |
| GSM80046 |
total RNA pool: 75% TR076, 25% TR077(16012165010012) |
| GSM80047 |
total RNA pool: 50% TR076, 50% TR077(16012165010013) |
| GSM80048 |
total RNA pool: 25% TR076, 75% TR077(16012165010014) |
| GSM80049 |
E12.5 Placenta1, 5 pooled(16012165010015) |
| GSM80050 |
E12.5 Embryos1, 5 pooled(16012165010016) |
| GSM80051 |
total RNA pool: 75% TR076, 25% TR077(16012165010017) |
| GSM80052 |
total RNA pool: 50% TR076, 50% TR077(16012165010018) |
| GSM80053 |
total RNA pool: 25% TR076, 75% TR077(16012165010019) |
| GSM80054 |
E12.5 Placenta1, 5 pooled(16012165010020) |
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| Relations |
| BioProject |
PRJNA93547 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE3508_RAW.tar |
284.7 Mb |
(http)(custom) |
TAR (of TIFF, TXT) |
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