|
| Status |
Public on May 09, 2018 |
| Title |
Paracancerous tissue 1-2 |
| Sample type |
RNA |
| |
|
| Source name |
Paracancerous tissue,surgery
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
tissue: Paracancerous tissue
age: 62y
|
| Extracted molecule |
total RNA |
| Extraction protocol |
LncRNAs/mRNAs were purified from total RNA after removal of rRNA (Arraystar rRNA removal kit).
|
| Label |
Cy3
|
| Label protocol |
Samples were 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 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 Axon GenePix 4000B microarray scanner.
|
| Description |
This sample is paired paracancerous tissue from a patient with gastric cancer
|
| Data processing |
Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and raw data extraction.Quantile normalization of raw data and subsequent data processing were performed using the R limma software package. The LncRNAs that at least 3 out of 6 samples have flag expressed (greater than 2 times background standard deviation) were retained for further differential analyses.
|
| |
|
| Submission date |
Mar 21, 2017 |
| Last update date |
May 09, 2018 |
| Contact name |
Junming Guo |
| E-mail(s) |
[email protected]
|
| Organization name |
Ningbo University
|
| Department |
Department of Biochemistry and Molecular Biology, and Zhejiang Provincial Key Laboratory of Pathophysiology
|
| Street address |
818 Fenghua Road
|
| City |
Ningbo |
| ZIP/Postal code |
315211 |
| Country |
China |
| |
|
| Platform ID |
GPL22937 |
| Series (1) |
| GSE96856 |
Metabolic pathways-associated lncRNA expression profiles of 6 human samples derived from patients with gastric cancer |
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