|
| Status |
Public on Jan 19, 2012 |
| Title |
heart male pbs 10 dpi rep1 |
| Sample type |
RNA |
| |
|
| Source name |
male heart 10 days post pbs injection
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/C
age: 8-10 weeks
treatment: PBS
gender: Male
time: 10 dpi
tissue: heart
|
| Treatment protocol |
Mice were treated with either PBS or heart-passaged CVB3 intraperitoneally. Mice were harvested at 10 days post infection and hearts were flash frozen in liquid nitrogen for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were homogenized in 2mL TRIzol according to the manufacturer's protocol. PureLink Micro-to-midi Total RNA purification System was used for extraction and purification of RNA
|
| Label |
Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (biotin)
|
| Label protocol |
RNAs were processed for hybridization to Affymetrix Mouse Gene ST 1.0 microarrays using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay, according to manufacturer's recommended protocol. One hundred nanograms of total RNA was amplified.
|
| |
|
| Hybridization protocol |
Hybridization cocktails were prepared as recommended for arrays of Mini/169 format using reagents in the Affymetrix Hybridization Wash Stain kit. Hybridization mix and fragmented, labeled ST-sscDNA were incubated at 99oC for 2 min and 45oC for 5 min, and then centrifuged at maximum speed for 5 min prior to pipetting into the GeneChips (Affymetrix Mouse Gene ST 1.0). Hybridization was performed at 45oC for 18 hours at 60RPM in the Affymetrix rotisserie hybridization oven. The signal amplification protocol for washing and staining of eukaryotic targets was performed in an automated fluidies station (Affymetrix FS450) using Affymetrix protocol FS450_0001.
|
| Scan protocol |
Arrays were transferred to a GCS3000 laser scanner with autoloader and 3G upgrade (Affymetrix) and scanned at an emission wavelength of 570nm at 2.5 um resolution
|
| Description |
Gene expression data of male hearts after a 10 day treatment of PBS
|
| Data processing |
CEL files were imported and analyzed with the default algorithm workflow RMA-Sketch, which includes RMA background correction, and Sketch-Quantile normalization.
The values recommended by Affymetrix as QC metrics include Positive vs. negative AUC (assessment of sensitivity and specificity), as well as all probeset mean and all probeset relative log expression.
|
| |
|
| Submission date |
Jan 18, 2012 |
| Last update date |
Jan 19, 2012 |
| Contact name |
DeLisa Fairweather |
| E-mail(s) |
[email protected]
|
| Phone |
4105023644
|
| Fax |
4109550116
|
| Organization name |
Johns Hopkins University
|
| Department |
Environmental Health Sciences
|
| Lab |
Fairweather Laboratory
|
| Street address |
615 N Wolfe St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE35182 |
Sex differences during acute myocarditis against coxsackievirus B3 (CVB3)-induced myocarditis (10 dpi) and chronic myocarditis/dilated cardiomyopathy (DCM) against CVB3-induced myocarditis (90 dpi) |
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