|
| Status |
Public on Mar 29, 2019 |
| Title |
AD-1 |
| Sample type |
RNA |
| |
|
| Source name |
hippocampal tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
group: Alzheimer's disease
tissue: Hippocampus
strain/background: SD
gender: Male
|
| Treatment protocol |
In this experiment, we utilized an intracerebroventricular (ICV) injection of Aβ1–42 oligomers into the cerebral ventricles of the animals to induce a validated AD model. For the control group, the vehicle was injected bilaterally into the lateral ventricles through a stainless steel cannula.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each hippocampal tissue sample by soaking the tissue samples in TRIzol Reagent (Invitrogen, Grand Island, NY, USA) in accordance with the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3′ bias via a random priming method (Arraystar Flash RNA Labelling Kit, Arraystar). The labelled cRNAs were purified using an RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labelled cRNAs (pmol Cy3/μg cRNA) were measured using the NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.
|
| Scan protocol |
Slides were scanned using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using homemade scripts.
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| |
|
| Submission date |
Mar 28, 2019 |
| Last update date |
Mar 29, 2019 |
| Contact name |
Weijun Peng |
| E-mail(s) |
pengweijun87@csu.edu.cn
|
| Phone |
8615874271876
|
| Organization name |
Central South University
|
| Department |
The Second Xiangya Hospital
|
| Street address |
No.139 Middle Renmin Road
|
| City |
Changsha |
| ZIP/Postal code |
410001 |
| Country |
China |
| |
|
| Platform ID |
GPL15690 |
| Series (1) |
| GSE129015 |
Distinct Hippocampal Expression Profiles of Long Non-coding RNAs in an Alzheimer’s Disease Model |
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