|
| Status |
Public on Aug 21, 2017 |
| Title |
Patient16_EGC |
| Sample type |
RNA |
| |
|
| Source name |
gastroscopic biopsy, patient16, EGC
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Patient 16
tissue: gastroscopic biopsy
age: 57
gender: Male
pathological stage: early gastric carcinoma (EGC)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using an RNeasy Mini Kit (Qiagen, MD, United States) following the manufacturers instructions. RNA concentration and integrity were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, USA) and an Agilent 2100 Bioanalyser (Agilent, CA, United States), respectively.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen, MD, United States). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600 ng 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 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray (G4851B) 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).
|
| Scan protocol |
Slides were scanned immediately after washing on Agilent SureScan Microarray Scanner (G2600D) using default settings for 8x60k array slides.
|
| Description |
Gene expression after gastroscopic biopsy
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol: GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity using GeneSpring GX v12.6.1 (Silicon Genetics, CA, USA) by its default settings.
|
| |
|
| Submission date |
Oct 05, 2016 |
| Last update date |
Aug 21, 2017 |
| Contact name |
li cheng Zhang |
| E-mail(s) |
zhang.chengli@163.com
|
| Organization name |
National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College
|
| Street address |
No. 17 Panjiayuan Nanli, Chaoyang District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100021 |
| Country |
China |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE87666 |
Gene expression profiling of human gastric tissues at different pathological stages |
|
