|
| Status |
Public on Mar 21, 2013 |
| Title |
Normal esophageal tissue from patient 1 with ESCC |
| Sample type |
RNA |
| |
|
| Source name |
surgical speciment from ESCC adjacent normal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal esophageal
gender: Male
age: 56
|
| Treatment protocol |
Primary tumours and adjacent non-neoplastic tissues were obtained from patients with esophageal squamous cell cancer who underwent surgical treatment, the samples were immeidately stored in liquid nitroge tank.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following manufacturer’s instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0 (Agilent) following manufacture's instruction, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004) 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 with acetonitrile for 1 min.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, 20 bit tiff file, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
normal esophageal tissue
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11and Grid:028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Mar 20, 2013 |
| Last update date |
Mar 21, 2013 |
| Contact name |
Wei Wu |
| E-mail(s) |
wuwei@ucalgary.ca
|
| Organization name |
1.Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China; 2. University of Calgary
|
| Street address |
3330 Hospital Dr. NW
|
| City |
Calgary |
| ZIP/Postal code |
T2N 4N1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE45350 |
Genome-wide screening of the expression of long noncoding RNA and coding RNA expression in esophageal sqaumous cell cancer |
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