|
| Status |
Public on Apr 01, 2020 |
| Title |
Brain_Sham_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
brain, sham, replicate 1
|
| Organism |
Mus musculus |
| Characteristics |
gender: male
age: 8 weeks
|
| Treatment protocol |
Mice subjected to tMCAO were sacrificed at 12 h after reperfusion. Total RNAs were extracted from the ischemia cortex of each mouse using TRIzol reagent.
|
| Growth protocol |
Mice were housed under a constant temperature and humidity and under a 12-hour light/12-hour dark cycle, with the lights on at 7:00 AM. Food and water were available ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresi
|
| Label |
Cy3
|
| Label protocol |
Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Description |
Gene expression in sham mouse-brain tissues
|
| 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 with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 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.
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| |
|
| Submission date |
Apr 28, 2017 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Bing Han |
| E-mail(s) |
bingh@seu.edu.cn
|
| Organization name |
Southeast University
|
| Street address |
Dingjiaqiao #87
|
| City |
Nanjing |
| ZIP/Postal code |
210009 |
| Country |
China |
| |
|
| Platform ID |
GPL19286 |
| Series (1) |
| GSE98319 |
Identification and characterization analysis of gene expression in mouse brain response to tMCAO |
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