|
| Status |
Public on Sep 10, 2013 |
| Title |
Hippocampus wild-type 1 |
| Sample type |
RNA |
| |
|
| Source name |
WT_hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain background: B6/SJL (for hemizygous 5xFAD mice) and C57BL/6J (for eIF2α+/S51A mice)
genotype/variation: wild-type
tissue: brain; hippocampus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA integrity was determined using a Bioanalyzer (Agilent) instrument. Only samples with RNA integrity numbers about 10 were processed on Affymetrix chips.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized on GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix).
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
01- 768 WT
|
| Data processing |
Chip images were inspected and checked for proper scanning. Raw data were then imported in Expression console (Affymetrix) to verify quality criteria (poly A controls, Hybridization controls and background to noise ratio) and to perform background correction, normalization and a RMA algorithm.
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.0.187
GeneSpring GX 10 software (Agilent) was further used for statistical evaluations and to generate clusters and heatmaps of the dataset.
|
| |
|
| Submission date |
Sep 02, 2013 |
| Last update date |
Sep 19, 2013 |
| Contact name |
Dan Ehninger |
| Organization name |
German Center for Neurodegenerative Diseases (DZNE)
|
| Street address |
Ludwig-Erhard-Allee 2
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53175 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6193 |
| Series (1) |
| GSE50521 |
Limited effects of an eIF2αS51A allele on neurological impairments in the 5xFAD mouse model of Alzheimer’s disease |
|
