|
| Status |
Public on Jun 04, 2020 |
| Title |
spleens_PBS_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
spleens, PBS, replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
gender: female
age: 12 weeks
|
| Treatment protocol |
EAE induction was performed using 2 mg/mL MOG35-55 immunization plus 200 ng pertussis toxin for each female C57BL/6 mouse via tail vein, and equivalent PBS instead of MOG35-55 was used as negative control. Spleen tissues were sepreated from three EAE model mice and three normal mice. Total RNAs were extracted from the spleen tissue 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 |
Total RNA was extracted from mouse spleen using Trizol reagent (Intrivogen) according to the manufacturer's instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| 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. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Description |
Gene expression in the normal mouse-spleen tissue
|
| 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.
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Zhengying Bian |
| E-mail(s) |
bzy_1995@yeah.net
|
| Phone |
15951835095
|
| Organization name |
China Pharmaceutical University
|
| Street address |
24 Tongjia Street
|
| City |
Nanjing |
| State/province |
Jiangsu Province |
| ZIP/Postal code |
210009 |
| Country |
China |
| |
|
| Platform ID |
GPL19286 |
| Series (1) |
| GSE151701 |
lncRNA and mRNA expression signatures for experimental autoimmune encephalomyelitis model mice and normal mice |
|
