|
| Status |
Public on Oct 25, 2016 |
| Title |
tissue_normal 471 |
| Sample type |
RNA |
| |
|
| Source name |
adjacent normal esophageal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: esophagus
gender: male
age: 58
tnm stage: Normal tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from human esophageal cancers and their matched adjacent normal tissues using Trizol following 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. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
1.0 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).
|
| Description |
mRNA and lncRNA expressison inadjacent normal esophageal 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 v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
|
| |
|
| Submission date |
Oct 24, 2016 |
| Last update date |
Oct 25, 2016 |
| Contact name |
Yuanyuan Wu |
| E-mail(s) |
82468097@qq.com
|
| Organization name |
Third Military Medical University
|
| Street address |
Sha ping ba
|
| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
| GSE89102 |
LncrRNA and mRNA expression profiling in human esophageal squamous cancer |
|
