|
| Status |
Public on Sep 05, 2013 |
| Title |
Ts1Cje-WT65-Hippocampus |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA from Hippocampus at 8-10 weeks of age
|
| Organism |
Mus musculus |
| Characteristics |
gender: female
genotype: WT
tissue: hippocampus
|
| Growth protocol |
Mice were housed in standard cages with food and water ad libitum under a controlled environment (temperature = 20°C; humidity = 60%) and a light/dark cycle of 12h. Ts1Cje males were backcrossed to C57Bl/6J females for several generations before experiments started.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ts1Cje females (N=6) and their wild-type littermates (N=5) were euthanized by cervical dislocation followed by decapitation. The cerebral cortex and the hippocampus were dissected on a cold platform and snap frozen in liquid nitrogen before storage at -80°C. Total RNA was isolated using the NucleoSpin RNA L and RNA II kits for the cortex and hippocampus respectively, following the manufacturer’s instructions (Macherey-Nagel, Bethlehem, PA). RNA concentrations were measured as absorbance at 260 nm on the Nanodrop instrument (Thermo Fisher Scientific, Waltham, MA). RNA quality was analyzed with the Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA) using the RNA 6000 Nano kit according to the manufacturer’s instructions. Only samples displaying an A260/A280 ratio of 2.0-2.1 and a RIN (RNA Integrity Number) > 9 were used for hybridization to the arrays.
|
| Label |
biotin
|
| Label protocol |
Samples were labeled with Biotin Allonamide Triphosphate according to the GeneChip Whole Transcriptome Labeling and Hybridization protocol (http://www.affymetrix.com) combining the Ambion WT Expression kit (Life Technologies, Grand Island, NY) and the Affymetrix GeneChip Terminal Labeling Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Arrays were washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
Arrays were scanned on a GeneArray Scanner 3000 7G, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
|
| Description |
Hippocampus gene expression data from mouse WT65
|
| Data processing |
Quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (Maastricht University, the Netherlands). Normalization was done using the Robust Multichip Average (RMA) algorithm and the MBNI custom CDF (http://brainarray.mbni.med.umich.edu/) version #14 for the mouse gene 1.0 ST array. Normalization output consisted of data for 21225 probe sets each corresponding to unique Entrez Gene IDs.
|
| |
|
| Submission date |
Aug 07, 2013 |
| Last update date |
Aug 05, 2014 |
| Contact name |
Heather C Wick |
| E-mail(s) |
[email protected]
|
| Organization name |
Tufts University
|
| Department |
Department of Computer Science
|
| Street address |
161 College Ave
|
| City |
Medford |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
| |
|
| Platform ID |
GPL13730 |
| Series (1) |
| GSE49635 |
Analysis of the Cerebral Cortex and Hippocampus Transcriptome Reveals Unique Molecular Changes in the Ts1Cje Mouse Model of Down Syndrome |
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