|
| Status |
Public on Jan 12, 2024 |
| Title |
cortex_control_1 |
| Sample type |
RNA |
| |
|
| Source name |
cortex, control condition
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: cortex
treatment: control
|
| Treatment protocol |
Half of the mice were submitted to a 6 hour SD performed by the so-called “gentle handling protocol”, starting at light onset (Zeitgeber Time 0). The other half was left undisturbed and used as control. At the end of the SD (ZT6), animals from both groups were sacrificed and brains were dissected and collected.For cortex and hippocampus dissection, two 2mm-thick sagittal slices taken 1mm lateral from the inter-hemispheric fissure were cut using a sagittal slicer matrix (Alto Stainless Matrices) in PBS (Life Technologies Europe). From the two resulting slices, hippocampi and cortex were dissected according to the Mouse Brain Atlas (Paxinos and Franklin, 2001).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brain tissues dissected from SD and control mice were homogenized in QIAzol Lysis Reagent (Qiagen). RNA was extracted and purified using the QIAGEN miRNeasy mini kit 50 (Qiagen) according to the manufacturer instructions. All RNA sample amounts were measured with a NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific) and the quality of RNA samples was verified on Agilent 2100 bioanalyzer chips (Agilent technologies).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (100ng) was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH), denaturated with dimethyl sulfoxide, and labeled with pCd-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH).
|
| |
|
| Hybridization protocol |
The labeled RNAs were hybridized to a Mouse miRNA Microarray (G4472B, Agilent Technologies) for 20h at 55°C with rotation. Samples were pooled per group of 2 animals for each condition (SD/control) and for each brain region (cortex/hippocampus), resulting in a total of 8 arrays.
|
| Scan protocol |
After hybridization and washing, the arrays were scanned with an Agilent microarray scanner using high dynamic range settings as specified by the manufacturer. Agilent Feature Extraction Software was used to extract the data.
|
| Data processing |
Data were normalized by a quantile normalization approach implemented in-house in the R programming language, as described in S. Pradervand et al., 2009, doi: 10.1261/rna.1295509.
|
| |
|
| Submission date |
Nov 22, 2021 |
| Last update date |
Jan 12, 2024 |
| Contact name |
Leonore Wigger |
| E-mail(s) |
[email protected]
|
| Organization name |
Swiss Institute of Bioinformatics
|
| Lab |
Vital-IT
|
| Street address |
Amphipôle Building
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL15547 |
| Series (2) |
| GSE189319 |
Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner [agilent_cortex_hippocampus] |
| GSE189353 |
Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner |
|
