|
| Status |
Public on Nov 10, 2018 |
| Title |
Pancreas_AP_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
pancreas, AP, replicate 2
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: pancreas
gender: male
age: 6 weeks
|
| Treatment protocol |
Retrograde pancreatic ductal administration of 1 mL/kg of 4% sodium taurocholate was used to induce the AP model. Animals were sacrificed after 9 h. Total RNAs were extracted from the pancreas of each rat using TRIzol reagent.
|
| Growth protocol |
Rats were habituated to a constant room temperature (25 ℃) under a 12:12 h light:dark cycle with ad libitum access to food and water.
|
| 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.
|
| 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 AP rat-pancreas 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 |
Nov 09, 2018 |
| Last update date |
Nov 10, 2018 |
| Contact name |
Jing Lin |
| E-mail(s) |
lin12301010073@163.com
|
| Phone |
18818264865
|
| Organization name |
Red House Hospital
|
| Street address |
Shanghai
|
| City |
Shanghai |
| State/province |
State... |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL15690 |
| Series (1) |
| GSE122379 |
Characteristics of long non-coding RNAs in the pancreas of rats with acute pancreatitis |
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