|
| Status |
Public on May 23, 2012 |
| Title |
Gastric cancer tissue sample [442T] |
| Sample type |
RNA |
| |
|
| Source name |
stomach
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 51
tissue type: Gastric Cancer Tissue
disease state: tumor
histopathology: adenocarcinoma
tumor stage: T2N0M0
differentiation: PD
|
| Treatment protocol |
25 pairs of gastric tissues were collected immediately after surgical resection and snap-frozen in liquid nitrogen. Microdissection was performed using MMI CellCut LCM system (MMI), under 100 × magnification. Tumor or non-malignant cells were captured from cancerous or adjacent noncancerous tissues using LCM macro caps (MMI), respectively.
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
One hundred nanograms of starting total RNAs was used in first round double strand (ds)-cDNA synthesis and cRNA synthesis; 8-10 μg of cRNA could be got and then used in second round single-strand (ss)-cDNA synthesis. ss-cDNA fragmentation and labeling were finished according to the Whole Transcript Sense Target Labeling Assay manual (Affymetrix).
|
| |
|
| Hybridization protocol |
Five micrograms of labeled ss-cDNA was used to hybridize the Human Exon 1.0 ST microarray for 16 hours. Staining and washing were all processed with Affymetrix’s protocols.
|
| Scan protocol |
The arrays were scanned on the GeneChip Scanner 3000 7G with GeneChip Operating Software v 1.3 (Affymetrix) to generate .CEL intensity files.
|
| Description |
tumor stomach sample
|
| Data processing |
Expression Consol software (v 1.0) (Affymetrix) integrated robust multiarray analysis (RMA) algorithm was applied to extract gene-level expression signal and detection above background (DABG) P-value for each probe set of the samples. Probe sets with P<0.05 were considered as present, and an expression signal cutoff was set as 3.9, as minimum number of falsely called probes. Only the genes with signal above cutoff were used in later analysis.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Oct 31, 2011 |
| Last update date |
May 23, 2012 |
| Contact name |
Cheng Lei |
| E-mail(s) |
chenglei_2008@126.com
|
| Organization name |
National Engineering Center for Biochip at Shanghai
|
| Street address |
151 Li Bing Road
|
| City |
Shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE33335 |
Expression data from gastric tissues: Cancer Samples vs. Matched Adjacent Noncancerous Samples |
| GSE33429 |
Cancer Samples vs. Matched Adjacent Noncancerous Samples |
|
