|
| Status |
Public on Dec 25, 2014 |
| Title |
Surgical sample of diffuse-type gastric cancer 06 |
| Sample type |
RNA |
| |
|
| Source name |
Gastric cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Diffuse-type gastric cancer tumor
|
| Treatment protocol |
All surgical samples were obtained from gastric cancer patients without neoadjuvant therapy. For the surgical samples, trained pathologists carefully excised bulk tissue samples from the main tumor, leaving a clear margin from the surrounding normal tissue. The samples were immediately frozen at -80 ﾟC until use. Frozen samples were placed in the ISOGEN solution (Nippon Gene, Toyama, Japan) and homogenised befor total RNA extraction.
|
| Growth protocol |
All gastric cancer tissues were provided by the National Cancer Center Hospital after obtaining written informed consent from each patient and approval by the Center’s Ethics Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ISOGEN extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
cRNA derived from 5 ug of total RNA was used to generate a byotinylated cRNA probe by T7-transcription. The procedures were conducted according to the supplier’s protocols.
|
| |
|
| Hybridization protocol |
We used human U95A oligonucleotide probe arrays (Affymetrix, Santa Clara, CA) for analysis of mRNA expression levels corresponding to 12,626 transcripts. Ten micrograms of fragmented cRNA were hybridized to the microarrays in 200 ul of a hybridization cocktail at 45 ℃ for 16 h in a rotisserie oven set at 60 rpm. The arrays were then washed with nonstringent wash buffer (6xSSPE) at 25 ℃, followed by stringent wash buffer (100 mM MES (pH6.7), 0.1 M NaCl, and 0.01% Tween 20) at 50 ℃, stained with streptavidin phycoerythrin (Molecular Probes), washed again with 6xSSPE, stained with biotinylated anti-streptavidin IgG, followed by a second staining with streptavidin phycoerythrin and a third wash with 6xSSPE.
|
| Scan protocol |
The arrays were scanned using the GeneArray scanner (Affymetrix) at 3-um resolution.
|
| Description |
Gene expression data using Human Expression Array U95AV2
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using default settings by Expression Console ver 1.1.
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| |
|
| Submission date |
May 16, 2013 |
| Last update date |
Dec 25, 2014 |
| Contact name |
Hiroki Sasaki |
| Organization name |
National Cancer Center Reseach Institute
|
| Street address |
Tukiji5-1-1
|
| City |
Chuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
104-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8300 |
| Series (1) |
| GSE47007 |
Expression data from intestinal-type and diffuse-type gastric cancers |
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