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Status |
Public on Apr 27, 2013 |
Title |
R26R^AC/AC (Control), biological replicate #3 |
Sample type |
RNA |
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Source name |
Mouse control_PSM
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Organism |
Mus musculus |
Characteristics |
strain background: C57BL6/6J genotype/variation: R26R^AC/AC (Control) developmental stage: E8.75 tissue: presomitic mesoderm (PSM)
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Treatment protocol |
The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).
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Growth protocol |
Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.
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Extracted molecule |
total RNA |
Extraction protocol |
The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).
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Label |
Biotin
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Label protocol |
Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).
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Hybridization protocol |
Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.
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Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
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Description |
Gene expression data from control PSM.
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Data processing |
Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).
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Submission date |
Apr 26, 2013 |
Last update date |
Apr 27, 2013 |
Contact name |
Timothy Peter Lopez |
E-mail(s) |
tpetelopez@gmail.com
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Organization name |
Johns Hopkins University/Carnegie Institution
|
Department |
Biology
|
Lab |
Chen-Ming Fan
|
Street address |
3520 San Martin Drive
|
City |
Baltimore |
State/province |
Maryland |
ZIP/Postal code |
21218 |
Country |
USA |
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Platform ID |
GPL1261 |
Series (1) |
GSE46426 |
The Presomitic Mesoderm (PSM) CREB family transcriptome |
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