|
| Status |
Public on Jun 25, 2024 |
| Title |
Derlin-1_KO_2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse dentate gyrus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Dentate gyrus
gender: male
strain: C57BL/6
genotype: Derlin-1flox/flox
|
| Treatment protocol |
Derlin-1_control was Derlin-1flox/flox, and Derlin-2_control was Derlin-2flox/flox. Mice expressing Cre recombinase driven by the nestin promoter were intercrossed with Derl1flox/flox mice and Derl2flox/flox mice respectively to generate Derlin-1_KO and Derlin-2_KO mice.
|
| Growth protocol |
C57BL/6 mice were raised under specific pathogen-free conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from mouse dentate gyrus were extracted using NucleoSpin RNA kit (TaKaRa Bio) according to the instructions. This included an on-column DNase digestion with the RNase-free Dnase (TaKaRa Bio)
|
| Label |
Cy3
|
| Label protocol |
For RNA amplification and labeling, we used Agilent Low-Input QuickAmp labeling kit (Agilent) according to the manufacture’s guidance. 150 ng of total RNA of each sample was amplified T7-RNA polymerase and simultaneously incorporated Cy3-labeled CTP.
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labeled cRNA was fragmented and hybridized onto the Agilent SurePrint G3 mouse GE 8 × 60K slide (design ID-074809), with rotating incubation at 65˚C for 17 h.
|
| Scan protocol |
Slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation, and scanned by the Agilent DNA Microarray scanner (G2505C).
|
| Description |
Gene expression
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data files were subjected to the GeneSpring (ver. 14.9) for analysis.
|
| |
|
| Submission date |
Apr 10, 2023 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Naoya Murao |
| E-mail(s) |
naoya_murao@med.miyazaki-u.ac.jp
|
| Organization name |
University of Miyazaki
|
| Department |
Medical Sciences
|
| Lab |
Biochemistry and Molecular Biology
|
| Street address |
Kihara5200
|
| City |
Miyazaki |
| ZIP/Postal code |
889-1692 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21163 |
| Series (1) |
| GSE229342 |
Gene expression profiling of hippocampal dentate gyrus in the central nervous system-specific Derlin-1 or Derlin-2 deficient mice |
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