|
| Status |
Public on Jan 10, 2013 |
| Title |
WT.VEH.24.709 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse brains
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: wild-type
agent: vehicle
time point: 24
gender: male
strain: C57BL6
age: Eleven-week-old
tissue: brain
|
| Biomaterial provider |
The University of Washington (Seattle, WA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA purification was performed as described (PMID: 19380167). Briefly, tissues were dissolved by low-power sonication in a solution consisting of 4 M guanidinium thiocyanate and 0.1 M 2-mercaptoethanol. After sonication, sodium acetate (pH 4), phenol (pH 4), and a 24:1 mix of chloroform and isoamylic acid were added on ice; after vigorous vortexing, aqueous solution containing total RNA was separated by high-speed centrifugation at 4 ?C for 20 min. RNA was precipitated by adding an equal volume of isopropanol, and it was stored at -20 ?C overnight and then, pelleted by centrifugation for 20 min at maximum speed at 4 ?C, rinsed with 70% ethanol, and resuspended in an appropriate volume of nuclease-free water.
|
| Label |
biotin
|
| Label protocol |
For microarray hybridization, RNA was processed for hybridization to GeneChip? Mouse Genome 430 2.0 Array through a core facility in the Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer?s instructions.
|
| |
|
| Hybridization protocol |
The standard hybridization protocol was used as recommended by Affymterix.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).
|
| Description |
Mouse brains.
|
| Data processing |
R/Bioconductor affy package, RMA normalization log2
|
| |
|
| Submission date |
Jan 12, 2011 |
| Last update date |
Sep 05, 2017 |
| Contact name |
James William MacDonald |
| E-mail(s) |
jmacdon@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Environmental and Occupational Health Sciences
|
| Street address |
4225 Roosevelt Way NE
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105-6099 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE26600 |
Cycad Genotoxin Methylazoxymethanol (MAM) Modulates Cellular Pathways Involved in Cancer and Neurodegenerative Disease |
|
