|
| Status |
Public on Oct 28, 2012 |
| Title |
WT Cardiomyocytes 16hr after doxorubicin rep1 |
| Sample type |
RNA |
| |
|
| Source name |
WT Cardiomyocytes 16hr after doxorubicin
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129SvEv/C57BL/6
gender: male
age: 6 weeks
genotype/variation: Top2b-/- (cardiac specific deletion of Top2b)
injected with: doxorubicin (25mg/kg, i.p.) or PBS (i.p.)
tissue: heart
cell type: primary cardiomyocytes
|
| Treatment protocol |
Mice were first injected with doxorubicin (25mg/kg, i.p.) or PBS (i.p.). Hearts were removed 16hr or 72 hr after injection. Live cardiomyocytes were isolated from the heart immediately by using a Langendorff aparatus.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the isolated cardiomyocytes with TRIZOL reagent (Invitrogen), RNA was then purified with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
One hundred nanograms of each total RNA sample were used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven
|
| Scan protocol |
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies)
|
| Description |
Gene expression 16 hr after Doxorubicin injection (i.p.)
16 hr WT Dox1
|
| Data processing |
The Agilent Feature Extraction Software (FES, Version 10.7.3.1) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Version 7.2)
|
| |
|
| Submission date |
Aug 22, 2012 |
| Last update date |
Oct 28, 2012 |
| Contact name |
Sui Zhang |
| Organization name |
U.T. M.D. Anderson Cancer Center
|
| Department |
Cardiology
|
| Street address |
1400 Pressler St.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77025 |
| Country |
USA |
| |
|
| Platform ID |
GPL13912 |
| Series (1) |
| GSE40289 |
Gene expression in the wildtype and top2b-deleted cardiomyocytes with or without doxorubicin treatment |
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