|
| Status |
Public on Dec 04, 2011 |
| Title |
Diffuse-type Gastric Cancer Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Diffuse-type gastric cancer
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Atp4b-Cre+;Cdh1loxP/loxP;Trp53loxP/loxP
age: 12 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Five normal gastric mucosae, from which stromas were removed mechanically in 30 mM EDTA-2Na, and three primary gastric cancers were obtained from Atp4b-Cre-;Cdh1loxP/loxP;Trp53loxP/loxP and Atp4b-Cre+;Cdh1loxP/loxP;Trp53loxP/loxP mice at 12 months, respectively. Total RNA from the tissues was isolated with TRIzol Reagent (Invitrogen, Carlsbad, CA). Contaminant DNA was removed by digestion with RNase-free DNase using DNA-free Kit (Applied Biosystems, Carlsbad, CA). Integrity of obtained RNA was assessed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples were confirmed to have an RNA Integrity Number (RIN) greater than 7.
|
| Label |
Cy5
|
| Label protocol |
Using 250 ng of total RNA, cRNA was prepared using Low RNA Input Fluorescent Linear Amplification Kit PLUS, Two-Color (Agilent), and labeled with Cy5 for three independent mouse DGC samples and Cy3 for a pool of five normal gastric mucosal samples.
|
| |
|
| Channel 2 |
| Source name |
pooled normal gastric mucosal tissues
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Atp4b-Cre-;Cdh1loxP/loxP;Trp53loxP/loxP
age: 12 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Five normal gastric mucosae, from which stromas were removed mechanically in 30 mM EDTA-2Na, and three primary gastric cancers were obtained from Atp4b-Cre-;Cdh1loxP/loxP;Trp53loxP/loxP and Atp4b-Cre+;Cdh1loxP/loxP;Trp53loxP/loxP mice at 12 months, respectively. Total RNA from the tissues was isolated with TRIzol Reagent (Invitrogen, Carlsbad, CA). Contaminant DNA was removed by digestion with RNase-free DNase using DNA-free Kit (Applied Biosystems, Carlsbad, CA). Integrity of obtained RNA was assessed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples were confirmed to have an RNA Integrity Number (RIN) greater than 7.
|
| Label |
Cy3
|
| Label protocol |
Using 250 ng of total RNA, cRNA was prepared using Low RNA Input Fluorescent Linear Amplification Kit PLUS, Two-Color (Agilent), and labeled with Cy5 for three independent mouse DGC samples and Cy3 for a pool of five normal gastric mucosal samples.
|
| |
|
| |
| Hybridization protocol |
Hybridization and signal detection of Mouse GE 4x44K v2 Microarray (G4122F, Agilent) was performed following the manufacturer's instructions.
|
| Scan protocol |
Scanned on an Agilent G2539A scanner.
|
| Description |
Biological replicate 2 of 3. Gastric cancer vs. normal gastric mucosal tissues.
|
| Data processing |
Gene expression data were acquired by Feature Extraction Software version 9.5.3 (Agilent) and were then transformed into log2 ratio of Cy5 / Cy3 for each gene. Probes that were marked as present in all three samples were used.
|
| |
|
| Submission date |
Nov 12, 2010 |
| Last update date |
Dec 04, 2011 |
| Contact name |
Kaoru Mogushi |
| E-mail(s) |
[email protected]
|
| Phone |
+81-3-5802-1797
|
| Organization name |
Juntendo University
|
| Department |
Intractable Disease Research Center
|
| Street address |
2-1-1 Hongo
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8421 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE25302 |
Synergistic Tumor Suppressor Activity of E-cadherin and p53 in a Conditional Mouse Model for Diffuse-Type Gastric Cancer |
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